> ## Documentation Index
> Fetch the complete documentation index at: https://10play-session-status-checl.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.
# Commands
> All 424 cmd.* commands with parameters and defaults.
424 commands, introspected from a live PyMOL. Call them through
`@tenmol/client` — e.g. `await cmd.color("red", "chainA")`.
### cmd.LockCM
### cmd.SafeEvalNS
### cmd.Shortcut
| Parameter | Type | Default | Description |
| --------------------------- | ---------- | ------- | ----------- |
| `keywords` | `Optional` | `None` | |
| `filter_leading_underscore` | `bool` | `True` | |
### cmd.abort
"abort" abruptly terminates execution of the PyMOL command script without executing any additional commands.
**See also:** `embed`, `skip`, `python`
### cmd.accept
"accept" is an internal method for handling of session file security.
### cmd.add\_bond
API-only function to add a bond by atom indices (1-based, same as "index" in cmd.iterate()). To add bonds by atom selection, use cmd.bond()
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ------------------------ |
| `oname` | `str` | | object name |
| `index1` | `int` | | first atom index |
| `index2` | `int` | | second atom index |
| `order` | `int` | `1` | bond order \{default: 1} |
**See also:** `cmd.get_bonds()`
### cmd.align
"align" performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit. "align" does a good job on proteins with decent sequence similarity (identity >30%). For comparing proteins with lower sequence identity, the "super" and "cealign" commands perform better.
| Parameter | Type | Default | Description |
| -------------- | -------- | ------------ | ----------------------------------------------------------- |
| `mobile` | `string` | | atom selection of mobile object |
| `target` | `string` | | atom selection of target object |
| `cutoff` | `float` | `2.0` | outlier rejection cutoff in Angstrom \{default: 2.0} |
| `cycles` | `int` | `5` | maximum number of outlier rejection cycles \{default: 5} |
| `gap` | | `-10.0` | |
| `extend` | | `-0.5` | |
| `max_gap` | | `50` | |
| `object` | `string` | `None` | name of alignment object to create \{default: (no |
| `matrix` | `string` | `'BLOSUM62'` | file name of substitution matrix for sequence |
| `mobile_state` | `int` | `0` | object state of mobile selection \{default: 0 = all states} |
| `target_state` | `int` | `0` | object state of target selection \{default: 0 = all states} |
| `quiet` | | `1` | |
| `max_skip` | | `0` | |
| `transform` | `0/1` | `1` | do superposition \{default: 1} |
| `reset` | | `0` | |
**See also:** `super`, `cealign`, `pair_fit`, `fit`, `rms`, `rms_cur`, `intra_rms`, `intra_rms_cur`
### cmd.alignto
"alignto" aligns all other loaded objects to the target using the specified alignment algorithm. This is a wrapper for "extra\_fit".
| Parameter | Type | Default | Description |
| ----------- | ----- | ----------- | ----------------------------------------------------------- |
| `target` | `str` | `''` | reference object name \{default: first object in selection} |
| `method` | `str` | `'cealign'` | (see "extra\_fit") \{default: cealign} |
| `selection` | `str` | `''` | (see "extra\_fit") \{default: public objects} |
| `quiet` | | `1` | |
**See also:** `extra_fit`, `align`, `super`, `cealign`, `fit`, `rms`, `rms_cur`, `intra_fit`
### cmd.alphatoall
Expand any given property of the CA atoms to all atoms in the residue
| Parameter | Type | Default | Description |
| ------------ | -------- | ----------- | ----------------------------------------------------- |
| `selection` | `string` | `'polymer'` | atom selection \{default: polymer} |
| `properties` | `string` | `'b'` | space separated list of atom properties \{default: b} |
| `operator` | | `'byca'` | |
| `quiet` | | `1` | |
### cmd.alter
"alter" changes atomic properties using an expression evaluated within a temporary namespace for each atom.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `selection` | | | |
| `expression` | | | |
| `quiet` | | `1` | |
| `space` | | `None` | |
**See also:** `alter_state`, `iterate`, `iterate_state`, `sort`
### cmd.alter\_list
"alter\_list" is an unsupported feature.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `object` | | | |
| `expr_list` | | | |
| `quiet` | | `1` | |
| `space` | | `None` | |
### cmd.alter\_state
"alter\_state" changes atom coordinates and flags over a particular state and selection using the Python evaluator with a temporary namespace for each atomic coordinate.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `state` | | | |
| `selection` | | | |
| `expression` | | | |
| `quiet` | | `1` | |
| `space` | | `None` | |
| `atomic` | | `1` | |
**See also:** `iterate_state`, `alter`, `iterate`
### cmd.angle
"angle" shows the angle formed between any three atoms.
| Parameter | Type | Default | Description |
| ------------ | ---- | --------- | ----------- |
| `name` | | `None` | |
| `selection1` | | `'(pk1)'` | |
| `selection2` | | `'(pk2)'` | |
| `selection3` | | `'(pk3)'` | |
| `mode` | | `None` | |
| `label` | | `1` | |
| `reset` | | `0` | |
| `zoom` | | `0` | |
| `state` | | `0` | |
| `quiet` | | `1` | |
| `state1` | | `-3` | |
| `state2` | | `-3` | |
| `state3` | | `-3` | |
**See also:** `distance`, `dihedral`
### cmd.api
API helper function. Get the full function name (incl. module) of given command.
| Parameter | Type | Default | Description |
| --------- | -------- | ------- | ----------------------- |
| `name` | `string` | | name of a PyMOL command |
### cmd.as\_pathstr
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `path` | | | |
### cmd.assign\_stereo
Assign "stereo" atom property (R/S stereochemistry). Requires either a Schrodinger Suite installation (SCHRODINGER environment variable set) or RDKit (rdkit Python module).
| Parameter | Type | Default | Description |
| ----------- | ----- | ---------- | ------------------------------------- |
| `selection` | `str` | `'all'` | atom selection \{default: all} |
| `state` | `int` | `-1` | object state \{default: -1 (current)} |
| `method` | | `''` | |
| `quiet` | | `1` | |
| `prop` | | `'stereo'` | |
### cmd.async\_
Run function threaded and show "please wait..." message.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `func` | | | |
### cmd.attach
"attach" adds a single atom on to the picked atom.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `element` | | | |
| `geometry` | | | |
| `valence` | | | |
| `name` | | `''` | |
| `quiet` | | `1` | |
### cmd.auto\_measure
### cmd.backward
"backward" moves the movie back one frame.
**See also:** `mset`, `forward`, `rewind`
### cmd.bg\_color
"bg\_color" sets the background color.
| Parameter | Type | Default | Description |
| --------- | -------- | --------- | -------------------------------------- |
| `color` | `string` | `'black'` | color name or number \{default: black} |
**See also:** `set_color`, `ray`
### cmd.bg\_colour
"bg\_color" sets the background color.
| Parameter | Type | Default | Description |
| --------- | -------- | --------- | -------------------------------------- |
| `color` | `string` | `'black'` | color name or number \{default: black} |
**See also:** `set_color`, `ray`
### cmd.block\_flush
### cmd.bond
"bond" creates a new bond between two selections, each of which should contain one atom.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ------------------------------------------------------- |
| `atom1` | `str` | `'pk1'` | Atom selection of first atom \{default: pk1} |
| `atom2` | `str` | `'pk2'` | Atom selection of second atom \{default: pk2} |
| `order` | `int` | `1` | Bond order \{default: 1} |
| `quiet` | | `1` | |
| `symop` | `str` | `''` | Symmetry operation code for second atom (e.g. "1\_555") |
**See also:** `unbond`, `fuse`, `attach`, `replace`, `remove_picked`
### cmd.button
"button" can be used to redefine what the mouse buttons do.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `button` | | | |
| `modifier` | | | |
| `action` | | | |
**See also:** `config_mouse`
### cmd.cache
"cache" manages storage of precomputed results, such as molecular surfaces.
| Parameter | Type | Default | Description |
| --------- | --------- | ------------ | --------------------------------------------------- |
| `action` | `string` | `'optimize'` | enable, disable, read\_only, clear, or optimize |
| `scenes` | `string` | `''` | a space-separated list of scene names (default: '') |
| `state` | `integer` | `-1` | state index (default: -1) |
| `quiet` | | `1` | |
### cmd.callout
Create a new screen-stabilized callout object.
| Parameter | Type | Default | Description |
| --------- | ----- | --------- | ----------- |
| `name` | `str` | | object name |
| `label` | `str` | | label text |
| `pos` | | `''` | |
| `screen` | | `'auto'` | |
| `state` | | `-1` | |
| `color` | | `'front'` | |
| `quiet` | | `1` | |
### cmd.capture
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.cartoon
"cartoon" changes the default cartoon representation for a set of atoms.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `type` | | | |
| `selection` | | `'(all)'` | |
### cmd.cd
"cd" changes the current working directory.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `dir` | | `'~'` | |
| `complain` | | `1` | |
| `quiet` | | `1` | |
**See also:** `pwd`, `ls`, `system`
### cmd.cealign
"cealign" aligns two proteins using the CE algorithm.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `target` | | | |
| `mobile` | | | |
| `target_state` | | `1` | |
| `mobile_state` | | `1` | |
| `quiet` | | `1` | |
| `guide` | | `1` | |
| `d0` | | `3.0` | |
| `d1` | | `4.0` | |
| `window` | | `8` | |
| `gap_max` | | `30` | |
| `transform` | | `1` | |
| `object` | | `None` | |
**See also:** `align`, `pair_fit`, `fit`, `rms`, `rms_cur`, `intra_rms`, `intra_rms_cur`, `super`
### cmd.center
"center" translates the window, the clipping slab, and the origin to a point centered within the atom selection.
| Parameter | Type | Default | Description |
| ----------- | -------- | ------- | ------------------------------------------------------ |
| `selection` | `string` | `'all'` | selection-expression or name pattern (default: "all"). |
| `state` | | `0` | |
| `origin` | | `1` | |
| `animate` | | `0` | |
**See also:** `origin`, `orient`, `zoom`
### cmd.centerofmass
Calculates the center of mass. Considers atom mass and occupancy.
| Parameter | Type | Default | Description |
| ----------- | --------- | --------- | ---------------------------------------------------- |
| `selection` | `string` | `'(all)'` | atom selection \{default: all} |
| `state` | `integer` | `-1` | object state, -1 for current state, 0 for all states |
| `quiet` | | `1` | |
**See also:** `get_extent`
### cmd.check
"check" is unsupported command that may eventually have something to do with assigning forcefield parameters to a selection of atoms.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | `None` | |
| `preserve` | | `0` | |
### cmd.clean
Run energy minimization on the given selection, using an MMFF94 force field.
| Parameter | Type | Default | Description |
| ----------- | ---- | -------- | ----------- |
| `selection` | | | |
| `present` | | `''` | |
| `state` | | `-1` | |
| `fix` | | `''` | |
| `restrain` | | `''` | |
| `method` | | `'mmff'` | |
| `async_` | | `0` | |
| `save_undo` | | `1` | |
| `message` | | `None` | |
### cmd.clip
"clip" alters the positions of the clipping planes.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `mode` | | | |
| `distance` | | | |
| `selection` | | `None` | |
| `state` | | `0` | |
**See also:** `zoom`, `orient`, `reset`
### cmd.cls
"cls" clears the output buffer.
### cmd.color
"color" changes the color of objects or atoms.
| Parameter | Type | Default | Description |
| ----------- | -------- | --------- | ------------------------------------ |
| `color` | `string` | | color name or number |
| `selection` | `string` | `'(all)'` | selection-expression or name-pattern |
| `quiet` | | `1` | |
| `flags` | | `0` | |
**See also:** `color_deep`, `set_color`, `recolor`
### cmd.color\_deep
Unset all object and atom level (not global) color settings and apply given color.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | -------------------------------------- |
| `color` | `str` | | color name or number |
| `name` | `str` | `'all'` | object name or pattern \{default: all} |
| `quiet` | | `1` | |
**See also:** `color`, `unset_deep`
### cmd.colour
"color" changes the color of objects or atoms.
| Parameter | Type | Default | Description |
| ----------- | -------- | --------- | ------------------------------------ |
| `color` | `string` | | color name or number |
| `selection` | `string` | `'(all)'` | selection-expression or name-pattern |
| `quiet` | | `1` | |
| `flags` | | `0` | |
**See also:** `color_deep`, `set_color`, `recolor`
### cmd.commands
### cmd.config\_mouse
"config\_mouse" sets the current mouse configuration ring.
| Parameter | Type | Default | Description |
| --------- | ---- | ---------------- | ----------- |
| `ring` | | `'three_button'` | |
| `quiet` | | `1` | |
**See also:** `mouse`, `button`
### cmd.contour\_sc
| Parameter | Type | Default | Description |
| --------- | ---- | ----------------------------------- | ----------- |
| `sc` | | `` | |
| `gnot` | | `` | |
### cmd.copy
"copy" creates a new object that is an identical copy of an existing object.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `target` | | | |
| `source` | | | |
| `zoom` | | `-1` | |
**See also:** `create`
### cmd.copy\_image
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.copy\_to
Copies selection to object `name` (all states) and by default renames chain, segi and ID identifiers to avoid naming conflicts.
| Parameter | Type | Default | Description |
| ----------- | ----- | ----------------- | --------------------------------------------- |
| `name` | `str` | | object name to modify |
| `selection` | `str` | | atom selection (will be copied to `name`) |
| `rename` | `str` | `'chain segi ID'` | space separated list of identifiers to rename |
| `zoom` | | `-1` | |
| `quiet` | | `1` | |
**See also:** `create`, `fuse`
### cmd.count\_atoms
"count\_atoms" returns a count of atoms in a selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
| `state` | | `0` | |
| `domain` | | `''` | |
### cmd.count\_discrete
Count the number of discrete objects in selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
| `quiet` | | `1` | |
### cmd.count\_frames
"count\_frames" returns the number of frames defined for the PyMOL movie.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
**See also:** `frame`, `count_states`
### cmd.count\_states
"count\_states" returns the number of states in the selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
**See also:** `frame`
### cmd.create
"create" creates a new molecule object from a selection. It can also be used to create states in an existing object.
| Parameter | Type | Default | Description |
| ----------------- | --------- | ------- | ----------------------------------------- |
| `name` | `string` | | name of object to create or modify |
| `selection` | `string` | | atoms to include in the new object |
| `source_state` | `integer` | `0` | \{default: 0 -- copy all states} |
| `target_state` | `integer` | `0` | -1 appends after last state \{default: 0} |
| `discrete` | | `0` | |
| `zoom` | | `-1` | |
| `quiet` | | `1` | |
| `singletons` | | `0` | |
| `extract` | | `None` | |
| `copy_properties` | | `False` | |
**See also:** `load`, `copy`, `extract`
### cmd.curve\_new
"curve\_new" creates a new curve object.
| Parameter | Type | Default | Description |
| ------------ | -------- | ---------- | ------------------------------------------------- |
| `name` | `string` | `''` | name of object to create |
| `curve_type` | `string` | `'bezier'` | type of curve (currently only "bezier" supported) |
### cmd.cycle\_valence
"cycle\_valence" cycles the valence on the currently selected bond.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `h_fill` | | `1` | |
| `quiet` | | `1` | |
**See also:** `remove_picked`, `attach`, `replace`, `fuse`, `h_fill`
### cmd.decline
"decline" is an internal method for handling of session file security.
### cmd.del\_colorection
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `dict` | | | |
| `key` | | | |
### cmd.delete
"delete" removes objects and named selections
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
**See also:** `remove`, `delete_states`
### cmd.delete\_states
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ----------------------------------------------- |
| `name` | `str` | | |
| `states` | `str` | | space separated list of state numbers or ranges |
**See also:** `delete`
### cmd.deprotect
"deprotect" reverses the effect of the "protect" command.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
**See also:** `protect`, `mask`, `unmask`, `mouse`, `editing`
### cmd.desaturate
Desaturate the colors in the given selection.
| Parameter | Type | Default | Description |
| ----------- | ----- | ------- | ------------------------------ |
| `selection` | `str` | `'all'` | atom selection \{default: all} |
| `a` | | `0.5` | |
| `quiet` | | `1` | |
### cmd.deselect
"deselect" disables any and all visible selections
### cmd.dihedral
"dihedral" shows dihedral angles formed between any four atoms.
| Parameter | Type | Default | Description |
| ------------ | ---- | --------- | ----------- |
| `name` | | `None` | |
| `selection1` | | `'(pk1)'` | |
| `selection2` | | `'(pk2)'` | |
| `selection3` | | `'(pk3)'` | |
| `selection4` | | `'(pk4)'` | |
| `mode` | | `None` | |
| `label` | | `1` | |
| `reset` | | `0` | |
| `zoom` | | `0` | |
| `state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `distance`, `angle`
### cmd.dirty
### cmd.dirty\_wizard
### cmd.disable
"disable" turns off display of one or more objects and/or selections.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | `'all'` | |
**See also:** `show`, `hide`, `enable`
### cmd.dist
"distance" creates a new distance object between two selections.
| Parameter | Type | Default | Description |
| ------------ | -------- | --------- | ------------------------------------------------ |
| `name` | `string` | `None` | name of the distance object to create |
| `selection1` | `string` | `'(pk1)'` | first atom selection |
| `selection2` | `string` | `'(pk2)'` | second atom selection |
| `cutoff` | `float` | `None` | longest distance to show |
| `mode` | `8` | `None` | like mode=3, but cutoff is the ratio between |
| `zoom` | | `0` | |
| `width` | | `None` | |
| `length` | | `None` | |
| `gap` | | `None` | |
| `label` | | `1` | |
| `quiet` | | `1` | |
| `reset` | | `0` | |
| `state` | `int` | `0` | object state to create the measurement object in |
| `state1` | | `-3` | |
| `state2` | | `-3` | |
### cmd.distance
"distance" creates a new distance object between two selections.
| Parameter | Type | Default | Description |
| ------------ | -------- | --------- | ------------------------------------------------ |
| `name` | `string` | `None` | name of the distance object to create |
| `selection1` | `string` | `'(pk1)'` | first atom selection |
| `selection2` | `string` | `'(pk2)'` | second atom selection |
| `cutoff` | `float` | `None` | longest distance to show |
| `mode` | `8` | `None` | like mode=3, but cutoff is the ratio between |
| `zoom` | | `0` | |
| `width` | | `None` | |
| `length` | | `None` | |
| `gap` | | `None` | |
| `label` | | `1` | |
| `quiet` | | `1` | |
| `reset` | | `0` | |
| `state` | `int` | `0` | object state to create the measurement object in |
| `state1` | | `-3` | |
| `state2` | | `-3` | |
### cmd.download\_chem\_comp
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `resn` | | | |
| `quiet` | | `1` | |
### cmd.drag
"drag" activates dragging for a selection, enabling the user to manipulate the atom coordinates of the atoms using mouse controls similar to those for controlling the camera.
| Parameter | Type | Default | Description |
| ----------- | -------- | ------- | --------------------------------------------- |
| `selection` | `string` | `None` | atoms to drag. If not provided, and dragging |
| `wizard` | | `1` | |
| `edit` | | `1` | |
| `quiet` | | `1` | |
| `mode` | | `-1` | |
### cmd.draw
"draw" creates an OpenGL-based image of the current frame.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `width` | | `0` | |
| `height` | | `0` | |
| `antialias` | | `-1` | |
| `quiet` | | `1` | |
**See also:** `ray`, `png`, `save`
### cmd.dss
"dss" defines secondary structure based on backbone geometry and hydrogen bonding patterns.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `state` | | `0` | |
| `context` | | `None` | |
| `preserve` | | `0` | |
| `quiet` | | `1` | |
### cmd.dump
The dump command writes the geometry of an isosurface, isomesh, isodot, or map object to a simple text file. Each line contains one vertex in case of representations, or one grid point in case of a map. For surface objects, XYZ coordinates and the normal are exported. Three lines make one triangle (like GL\_TRIANGLES). For mesh objects, XYZ coordinates are exported (no normals). The vertices form line strips (like GL\_LINE\_STRIP), a blank line starts a new strip.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `fnam` | | | |
| `obj` | | | |
| `state` | | `1` | |
| `quiet` | | `1` | |
**See also:** `COLLADA export`
### cmd.edit
"edit" picks atoms or a bond for editing.
| Parameter | Type | Default | Description |
| ------------ | ---- | -------- | ----------- |
| `selection1` | | `''` | |
| `selection2` | | `'none'` | |
| `selection3` | | `'none'` | |
| `selection4` | | `'none'` | |
| `pkresi` | | `0` | |
| `pkbond` | | `1` | |
| `quiet` | | `1` | |
**See also:** `unpick`, `remove_picked`, `cycle_valence`, `torsion`
### cmd.edit\_mode
"edit\_mode" switches the mouse into editing mode, if such a mode is available in the current mouse ring.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `active` | | `1` | |
| `quiet` | | `1` | |
### cmd.editing\_ring
Helper function for copy/cut/paste of molecular selections.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `action` | | | |
### cmd.enable
"enable" turns on display of one or more objects and/or selections.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | `'all'` | |
| `parents` | | `0` | |
**See also:** `show`, `hide`, `disable`
### cmd.ending
"ending" goes to the end of the movie.
### cmd.exp\_path
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `path` | | | |
### cmd.extendaa
API-only function to decorate a function as a PyMOL command with argument auto-completion.
### cmd.extra\_fit
Like "intra\_fit", but for multiple objects instead of multiple states.
| Parameter | Type | Default | Description |
| ----------- | -------- | --------- | ----------------------------------------------------------- |
| `selection` | `string` | `'(all)'` | atom selection of multiple objects \{default: all} |
| `reference` | `string` | `''` | reference object name \{default: first object in selection} |
| `method` | `string` | `'align'` | alignment method (command that takes "mobile" and "target" |
| `zoom` | | `1` | |
| `quiet` | | `0` | |
**See also:** `align`, `super`, `cealign`, `intra_fit`, `util.mass_align`
### cmd.extract
"extract" is simply a shorthand way calling the "create" command with the extract argument activated, so that atoms in the new object are removed from the source object.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `name` | | | |
| `selection` | | | |
**See also:** `create`
### cmd.fab
Build a peptide
| Parameter | Type | Default | Description |
| --------- | ----- | ----------- | ------------------------------------------------------------------------------- |
| `input` | `str` | | sequence in one-letter code |
| `name` | `str` | `None` | name of object to create \{default: } |
| `mode` | | `'peptide'` | |
| `resi` | | `1` | |
| `chain` | | `''` | |
| `segi` | | `''` | |
| `state` | | `-1` | |
| `dir` | | `1` | |
| `hydro` | | `-1` | |
| `ss` | `int` | `0` | Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat |
| `async_` | | `0` | |
| `quiet` | | `1` | |
### cmd.fast\_minimize
"fast\_minimize" is an unsupported nonfunctional command that may eventually have something to do with doing a quick clean up of the molecular structure.
### cmd.fb\_action
### cmd.fb\_mask
### cmd.fb\_module
### cmd.feedback
"feedback" changes the amount of information output by pymol.
| Parameter | Type | Default | Description |
| --------- | -------- | ------- | ------------------------------------------------------------------ |
| `action` | | `'?'` | |
| `module` | `string` | `'?'` | a space-separated list of modules or simply "all" |
| `mask` | `string` | `'?'` | a space-separated list of output categories or simply "everything" |
### cmd.fetch
"fetch" downloads a file from the internet (if possible)
| Parameter | Type | Default | Description |
| ----------- | ----- | ------- | ----------------------------------------------------- |
| `code` | | | |
| `name` | | `''` | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `-1` | |
| `multiplex` | | `-2` | |
| `zoom` | | `-1` | |
| `type` | `str` | `''` | cif, bcif, pdb, pdb1, 2fofc, fofc, emd, cid, sid |
| `async_` | `0/1` | `0` | download in the background and do not block the PyMOL |
| `path` | | `''` | |
| `file` | | `None` | |
| `quiet` | | `1` | |
### cmd.file\_read
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `finfo` | | | |
### cmd.filename\_to\_objectname
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `fname` | | | |
### cmd.find\_pairs
API only function. Returns a list of atom pairs. Atoms are represented as (model,index) tuples. Can be restricted to hydrogen-bonding-like contacts. WARNING: Only checks atom orientation, not atom type (so would hydrogen bond between carbons for example), so make sure to provide appropriate atom selections.
| Parameter | Type | Default | Description |
| ------------ | --------- | ------- | -------------------------------------------------------------- |
| `selection1` | | | |
| `selection2` | | | |
| `state1` | | `1` | |
| `state2` | | `1` | |
| `cutoff` | `float` | `3.5` | distance cutoff \{default: 3.5} |
| `mode` | `integer` | `0` | if mode=1, do coarse hydrogen bonding assessment \{default: 0} |
| `angle` | `float` | `45` | hydrogen bond angle cutoff, only if mode=1 \{default: 45.0} |
### cmd.finish\_object
"finish\_object" is used in cases where many individual states are being loaded and it is advantageos to avoid processing them until all states have been loaded into RAM. This function should always be called after loading an object with the finish flag set to zero.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
### cmd.fit
"fit" superimposes the model in the first selection on to the model in the second selection. Only matching atoms in both selections will be used for the fit.
| Parameter | Type | Default | Description |
| -------------- | --------- | ------- | -------------------------------------------------------------- |
| `mobile` | `string` | | atom selection |
| `target` | `string` | | atom selection |
| `mobile_state` | `integer` | `0` | object state \{default=0, all states) |
| `target_state` | `integer` | `0` | object state \{default=0, all states) |
| `quiet` | | `1` | |
| `matchmaker` | `integer` | `0` | how to match atom pairs \{default: 0} |
| `cutoff` | `float` | `2.0` | outlier rejection cutoff (only if cycles>0) \{default: 2.0} |
| `cycles` | `integer` | `0` | number of cycles in outlier rejection refinement \{default: 0} |
| `object` | `string` | `None` | name of alignment object to create \{default: None} |
**See also:** `align`, `super`, `pair_fit`, `rms`, `rms_cur`, `intra_fit`, `intra_rms`, `intra_rms_cur`
### cmd.fix\_chemistry
"fix chemistry" is an unsupported feature.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `selection1` | | `'all'` | |
| `selection2` | | `'all'` | |
| `invalidate` | | `1` | |
| `quiet` | | `1` | |
### cmd.flag
"flag" sets the indicated flag for atoms in the selection and clears the indicated flag for atoms not in the selection.
| Parameter | Type | Default | Description |
| ----------- | ------- | --------- | ---------------------------------------------------------------- |
| `flag` | | | |
| `selection` | `str` | | atom selection |
| `action` | `clear` | `'reset'` | clear the flag for selected atoms, leaving other atoms unchanged |
| `quiet` | | `1` | |
### cmd.fnab
Builds a nucleotide acid from sequence Fragments provided by: Lu, Xiang-Jun, Olson, Wilma K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures, Nucleic Acids Research, 32, W667-W675 (2004).
| Parameter | Type | Default | Description |
| ----------- | ----- | ------- | -------------------------------------------- |
| `input` | `str` | | Sequence as an array of one letter codes |
| `name` | `str` | `None` | Name of the object to create \{default: obj} |
| `mode` | `str` | `'DNA'` | "DNA" or "RNA" |
| `form` | `str` | `'B'` | "A" or "B" |
| `dbl_helix` | | `1` | |
### cmd.focal\_blur
Creates fancy figures by introducing a focal blur to the image. The object at the origin will be in focus.
| Parameter | Type | Default | Description |
| ---------- | ------- | ------- | --------------------------------------------- |
| `aperture` | `float` | `2.0` | aperture angle in degrees \{default: 2.0} |
| `samples` | `int` | `10` | number of images for averaging \{default: 10} |
| `ray` | `0/1` | `0` | \{default: 0} |
| `filename` | `str` | `''` | write image to file \{default: temporary} |
| `quiet` | | `1` | |
### cmd.forward
"forward" moves the movie one frame forward.
**See also:** `mset`, `backward`, `rewind`
### cmd.fragment
"fragment" retrieves a 3D structure from the fragment library, which is currently pretty meager (just amino acids).
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `object` | | `None` | |
| `origin` | | `1` | |
| `zoom` | | `0` | |
| `quiet` | | `1` | |
### cmd.frame
"frame" sets the viewer to the indicated movie frame.
| Parameter | Type | Default | Description |
| --------- | --------- | ------- | ----------------------- |
| `frame` | `integer` | | frame number to display |
| `trigger` | | `-1` | |
| `scene` | | `0` | |
**See also:** `count_states`
### cmd.full\_screen
"full\_screen" enables or disables full screen mode.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `toggle` | | `-1` | |
### cmd.fuse
"fuse" joins two objects into one by forming a bond. A copy of the object containing the first atom is moved so as to form an approximately resonable bond with the second, and that copy is then merged with the first object.
| Parameter | Type | Default | Description |
| ------------ | ------ | --------- | -------------------------------------------------- |
| `selection1` | `str` | `'(pk1)'` | single atom selection (will be copied to object 2) |
| `selection2` | `str` | `'(pk2)'` | single atom selection |
| `mode` | `int` | `0` | \{default: 0} |
| `recolor` | `bool` | `1` | recolor C atoms to match target \{default: 1} |
| `move` | `bool` | `1` | \{default: 1} |
**See also:** `bond`, `unbond`, `attach`, `replace`, `fuse`, `remove_picked`
### cmd.get
"get" prints out the current value of a setting.
| Parameter | Type | Default | Description |
| ----------- | --------- | ------- | ------------------------------------------ |
| `name` | `string` | | setting name |
| `selection` | `string` | `''` | object name (selections not yet supported) |
| `state` | `integer` | `0` | state number |
| `quiet` | | `1` | |
**See also:** `set`, `set_bond`, `get_bond`
### cmd.get\_angle
"get\_angle" returns the angle between three atoms. By default, the coordinates used are from the current state, however an alternate state identifier can be provided.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `atom1` | | `'pk1'` | |
| `atom2` | | `'pk2'` | |
| `atom3` | | `'pk3'` | |
| `state` | | `-1` | |
| `quiet` | | `1` | |
### cmd.get\_area
Get the surface area of an selection. Depends on the "dot\_solvent" setting. With "dot\_solvent=off" (default) it calculates the solvent excluded surface area, else the surface accessible surface.
| Parameter | Type | Default | Description |
| ----------- | ------ | --------- | ------------------------------------------------------ |
| `selection` | | `'(all)'` | |
| `state` | | `1` | |
| `load_b` | `bool` | `0` | store per-atom surface area in b-factors \{default: 0} |
| `quiet` | | `1` | |
**See also:** `"dot_solvent" setting`, `"dots" representation (show dots)`
### cmd.get\_assembly\_ids
EXPERIMENTAL AND SUBJECT TO CHANGE! Get the list of assembly ids for an object loaded from mmCIF.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `quiet` | | `1` | |
### cmd.get\_atom\_coords
"get\_atom\_coords" returns the 3D coordinates of a single atom.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
| `state` | | `0` | |
| `quiet` | | `1` | |
### cmd.get\_bond
"get\_bond" gets per-bond settings for all bonds which exist between two selections of atoms.
| Parameter | Type | Default | Description |
| ------------ | -------- | ------- | --------------------------------------------- |
| `name` | `string` | | name of the setting |
| `selection1` | `string` | | first set of atoms |
| `selection2` | `string` | `None` | seconds set of atoms \{default: (selection1)} |
| `state` | | `0` | |
| `updates` | | `1` | |
| `quiet` | | `1` | |
### cmd.get\_bond\_print
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `obj` | | | |
| `max_bond` | | | |
| `max_type` | | | |
### cmd.get\_bonds
Get a list of (atm1, atm2, order) tuples for bonds with coordinates in the given state (same logic as cmd.get\_model()). WARNING: atm1/atm2 are 0-based indices! They enumerate the atoms in the selection and do not necessarily correspond to the "index" atom property. To get a atm1/atm2 to index mapping, you can do: >>> stored.indices = \[] >>> cmd.iterate\_state(state, selection, "stored.indices.append(index)")
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `state` | | `-1` | |
**See also:** `cmd.get_model().bond`
### cmd.get\_bytes
API-only function which exports the selection to a molecular file format and returns it as a binary ("bytes") string.
| Parameter | Type | Default | Description |
| ----------- | ----- | --------- | ------------------------------------------------------ |
| `format` | `str` | | pdb\|cif\|sdf\|mol\|mol2\|mae\|pqr\|xyz |
| `selection` | `str` | `'(all)'` | atom selection \{default: all} |
| `state` | `int` | `-1` | object state (-1=current, 0=all) \{default: -1} |
| `ref` | `str` | `''` | object name which defines reference frame \{default: } |
| `ref_state` | `int` | `-1` | state of ref object \{default: -1} |
| `multi` | `int` | `-1` | for multi-entry file formats, 0 = single entry, |
| `quiet` | | `1` | |
### cmd.get\_chains
Print the list of chain identifiers in the given selection.
| Parameter | Type | Default | Description |
| ----------- | ----- | --------- | ------------------------------ |
| `selection` | `str` | `'(all)'` | atom selection \{default: all} |
| `state` | `int` | `0` | CURRENTLY IGNORED |
| `quiet` | | `1` | |
### cmd.get\_cifstr
API-only function which returns a mmCIF string.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | `'all'` | |
| `state` | | `-1` | |
| `quiet` | | `1` | |
**See also:** `get_pdbstr`
### cmd.get\_clip
"get\_clip" returns the positions of the clipping planes.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ----------- |
| `quiet` | `int` | `1` | |
**See also:** `clip`
### cmd.get\_collada
"get\_collada" returns a COLLADA string representing the content currently displayed.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `version` | | `2` | |
### cmd.get\_color\_index
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `color` | | | |
### cmd.get\_color\_indices
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `all` | | `0` | |
### cmd.get\_color\_tuple
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `mode` | | `0` | |
### cmd.get\_colorection
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `key` | | | |
### cmd.get\_coords
API only. Get selection coordinates as numpy array.
| Parameter | Type | Default | Description |
| ----------- | ----- | ------- | -------------------------------------------------- |
| `selection` | `str` | `'all'` | atom selection \{default: all} |
| `state` | `int` | `1` | state index or all states if state=0 \{default: 1} |
| `quiet` | | `1` | |
### cmd.get\_coordset
API only. Get object coordinates as numpy array.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | -------------------------------------------------------------- |
| `name` | | | |
| `state` | `int` | `1` | state index \{default: 1} |
| `copy` | `0/1` | `1` | \{default: 1} WARNING: only use copy=0 if you know what you're |
| `quiet` | | `1` | |
### cmd.get\_dihedral
"get\_dihedral" returns the dihedral angle between four atoms. By default, the coordinates used are from the current state, however an alternate state identifier can be provided. By convention, positive dihedral angles are right-handed (looking down the atom2-atom3 axis).
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `atom1` | | `'pk1'` | |
| `atom2` | | `'pk2'` | |
| `atom3` | | `'pk3'` | |
| `atom4` | | `'pk4'` | |
| `state` | | `-1` | |
| `quiet` | | `1` | |
### cmd.get\_distance
"get\_distance" returns the distance between two atoms. By default, the coordinates used are from the current state, however an alternate state identifier can be provided.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `atom1` | | `'pk1'` | |
| `atom2` | | `'pk2'` | |
| `state` | | `-1` | |
| `quiet` | | `1` | |
### cmd.get\_drag\_object\_name
### cmd.get\_editor\_scheme
### cmd.get\_extent
"get\_extent" returns the minimum and maximum XYZ coordinates of a selection as an array: \[ \[ min-X , min-Y , min-Z ],\[ max-X, max-Y , max-Z ]]
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `state` | | `0` | |
| `quiet` | | `1` | |
### cmd.get\_fastastr
API only. Get protein and nucleic acid sequences in fasta format. Used for saving: PyMOL> save foo.fasta New in PyMOL 2.2: - chain specific keys (key argument) - nucleic acid support
| Parameter | Type | Default | Description |
| ----------- | ----- | ------- | ------------------------------------------------------------ |
| `selection` | `str` | `'all'` | atom selection (reduced to "guide & alt +A") \{default: all} |
| `state` | `int` | `-1` | (only used if state > 0) |
| `quiet` | `0/1` | `1` | UNUSED |
| `key` | `str` | `''` | python expression \{default: model + "\_" + chain} |
### cmd.get\_frame
"get\_frame" returns the current frame index (1-based)
**See also:** `get_state`
### cmd.get\_gltf
"get\_gltf" saves a gltf file representing the content currently displayed.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `filename` | | | |
| `quiet` | | `1` | |
### cmd.get\_idtf
"get\_idft" is under development, but should eventually return an idtf file containing multiple objects and scenes.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.get\_legal\_name
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
### cmd.get\_modal\_draw
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.get\_model
"get\_model" returns a ChemPy "Indexed" format model from a selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `state` | | `1` | |
| `ref` | | `''` | |
| `ref_state` | | `0` | |
### cmd.get\_movie\_length
"get\_movie\_length" returns the number of frames explicitly defined in the movie, not including molecular states.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
| `images` | | `-1` | |
**See also:** `frame`, `count_states`, `count_frames`
### cmd.get\_movie\_locked
### cmd.get\_movie\_playing
### cmd.get\_mtl\_obj
NOTE: this is an incomplete and unsupported feature. "get\_mtl\_obj" returns a tuple containing mtl and obj input files for use with Maya.
### cmd.get\_names
"get\_names" returns a list of object and/or selection names.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------------------ | ----------- |
| `type` | | `'public_objects'` | |
| `enabled_only` | | `0` | |
| `selection` | | `''` | |
**See also:** `get_type`, `count_atoms`, `count_states`
### cmd.get\_names\_of\_type
"get\_names\_of\_type" will return a list of names for the given type.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `type` | | | |
| `public` | | `1` | |
### cmd.get\_object\_color\_index
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
### cmd.get\_object\_list
"get\_object\_list" is an unsupported command that may have something to do with querying the objects covered by a selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
### cmd.get\_object\_matrix
"get\_object\_matrix" is an unsupported command that may have something to do with querying the transformation matrices associated with an object
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `object` | | | |
| `state` | | `1` | |
| `incl_ttt` | | `1` | |
### cmd.get\_object\_settings
"get\_object\_settings" is an unsupported command
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | | |
| `state` | | `0` | |
| `quiet` | | `1` | |
### cmd.get\_object\_state
Returns the effective object state.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
### cmd.get\_object\_ttt
"get\_object\_ttt" is an unsupported command
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | | |
| `quiet` | | `1` | |
### cmd.get\_pdbstr
"get\_pdbstr" in an API-only function which returns a pdb corresponding to the atoms in the selection provided and that are present in the indicated state
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | `'all'` | |
| `state` | | `-1` | |
| `ref` | | `''` | |
| `ref_state` | | `-1` | |
| `quiet` | | `1` | |
### cmd.get\_phipsi
| Parameter | Type | Default | Description |
| ----------- | ---- | ------------- | ----------- |
| `selection` | | `'(name CA)'` | |
| `state` | | `-1` | |
### cmd.get\_position
"get\_position" returns the 3D coordinates of the center of the viewer window.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.get\_povray
"get\_povray" returns a tuple corresponding to strings for a PovRay input file.
### cmd.get\_progress
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `reset` | | `0` | |
### cmd.get\_property
Get an object-level property
| Parameter | Type | Default | Description |
| ---------- | -------- | ------- | ---------------------------------------------------- |
| `propname` | `string` | | Name of the property |
| `name` | `string` | | Name of a single object |
| `state` | `int` | `0` | Object state, 0 for all states, -1 for current state |
| `quiet` | | `1` | |
### cmd.get\_property\_list
Get all properties for an object (for a particular state) as a list
| Parameter | Type | Default | Description |
| --------- | -------- | ------- | ---------------------------------------------------- |
| `object` | `string` | | Name of a single object |
| `state` | `int` | `0` | Object state, 0 for all states, -1 for current state |
| `quiet` | | `1` | |
### cmd.get\_raw\_alignment
"get\_raw\_alignment" returns a list of lists of (object,index) tuples containing the raw per-atom alignment relationships
| Parameter | Type | Default | Description |
| ------------- | ---- | ------- | ----------- |
| `name` | | `''` | |
| `active_only` | | `0` | |
### cmd.get\_renderer
Prints OpenGL renderer information.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.get\_sasa\_relative
Calculates the relative per-residue solvent accessible surface area and optionally labels and colors residues. The value is relative to full exposure of the residue, calculated by removing all other residues except its two next neighbors, if present. Loads a value beteween 0.0 (fully buried) and 1.0 (fully exposed) into the b-factor property, available in "iterate", "alter" and "label" as "b".
| Parameter | Type | Default | Description |
| ----------- | ----- | ------- | ---------------------------------------------------------- |
| `selection` | `str` | `'all'` | atom selection \{default: all} |
| `state` | `int` | `1` | object state \{default: 1} |
| `vis` | `0/1` | `-1` | show labels and do color by exposure \{default: !quiet} |
| `var` | `str` | `'b'` | name of property to assign \{default: b} |
| `quiet` | `0/1` | `1` | print results to log window |
| `outfile` | `str` | `''` | filename, write to file instead of log window \{default: } |
| `subsele` | `str` | `'all'` | Sub-selection, e.g. "sidechain" \{default: all} |
**See also:** `get_area with "load_b=1" argument.`
### cmd.get\_scene\_list
### cmd.get\_scene\_message
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
### cmd.get\_scene\_thumbnail
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
### cmd.get\_selection\_state
Returns the effective object state for all objects in given selection. Raises exception if objects are in different states.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
### cmd.get\_session
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `names` | | `''` | |
| `partial` | | `0` | |
| `quiet` | | `1` | |
| `compress` | | `-1` | |
| `cache` | | `-1` | |
| `binary` | | `-1` | |
| `version` | | `-1` | |
### cmd.get\_setting\_boolean
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `object` | | `''` | |
| `state` | | `0` | |
### cmd.get\_setting\_float
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `object` | | `''` | |
| `state` | | `0` | |
### cmd.get\_setting\_int
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `object` | | `''` | |
| `state` | | `0` | |
### cmd.get\_setting\_legacy
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `object` | | `''` | |
| `state` | | `0` | |
### cmd.get\_setting\_text
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `object` | | `''` | |
| `state` | | `0` | |
### cmd.get\_setting\_tuple
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `object` | | `''` | |
| `state` | | `0` | |
### cmd.get\_setting\_updates
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | `''` | |
| `state` | | `0` | |
### cmd.get\_state
"get\_state" returns the current state index (1-based)
**See also:** `get_frame`
### cmd.get\_str
Like "get\_bytes" but return a unicode string.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `format` | | | |
| `selection` | | `'(all)'` | |
| `state` | | `-1` | |
| `ref` | | `''` | |
| `ref_state` | | `-1` | |
| `multi` | | `-1` | |
| `quiet` | | `1` | |
### cmd.get\_symmetry
"get\_symmetry" can be used to obtain the crystal and spacegroup parameters for a molecule or map.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `state` | | `-1` | |
| `quiet` | | `1` | |
### cmd.get\_title
"get\_title" retrieves a text string to the state of a particular object which will be displayed when the state is active.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | | |
| `state` | | | |
| `quiet` | | `1` | |
### cmd.get\_type
"get\_type" returns a string describing the named object or selection.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `quiet` | | `1` | |
**See also:** `get_names`
### cmd.get\_unused\_name
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `prefix` | | `'tmp'` | |
| `alwaysnumber` | | `1` | |
### cmd.get\_version
"get\_version" returns a tuple of length six containing text, floating point, and integer representations of the current PyMOL version number, build date as unix timestamp, GIT SHA and SVN code revision so far available.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.get\_view
"get\_view" returns and optionally prints out the current view information in a format which can be embedded into a command script and can be used in subsequent calls to "set\_view". If a log file is currently open, get\_view will not write the view matrix to the screen unless the "output" parameter is 2.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------------------------------------- |
| `output` | `3` | `1` | return formatted string instead of a list |
| `quiet` | | `1` | |
**See also:** `set_view`
### cmd.get\_viewport
"get\_viewport" returns and optionally prints out the screen viewport size
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------------------------------------------- |
| `output` | `2` | `1` | force output to screen even if log file is open |
| `quiet` | | `1` | |
### cmd.get\_vis
### cmd.get\_volume\_field
EXPERIMENTAL AND SUBJECT TO CHANGE - DO NOT USE API only. Get the raw data of a map or volume object.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | -------------------------------------------------------------- |
| `objName` | `str` | | object name |
| `state` | `int` | `1` | state index \{default: 1} |
| `copy` | `0/1` | `1` | \{default: 1} WARNING: only use copy=0 if you know what you're |
### cmd.get\_volume\_histogram
API ONLY. Get min, max, mean, stdev and histogram of a map or volume object as a list of length bins + 4.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `objName` | | | |
| `bins` | | `64` | |
| `range` | | `None` | |
### cmd.get\_vrml
"get\_vrml" returns a VRML2 string representing the content currently displayed.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `version` | | `2` | |
### cmd.get\_wizard
### cmd.get\_wizard\_stack
### cmd.gradient
"gradient" creates a gradient object from a map object.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `name` | | | |
| `map` | | | |
| `minimum` | | `1.0` | |
| `maximum` | | `-1.0` | |
| `selection` | | `''` | |
| `buffer` | | `0.0` | |
| `state` | | `0` | |
| `carve` | | `None` | |
| `source_state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `load`, `isomesh`
### cmd.group
"group" creates or updates a group object: a container for organizing objects into a hierarchy.
| Parameter | Type | Default | Description |
| --------- | -------- | -------- | --------------------------------------------- |
| `name` | `string` | | name of the group |
| `members` | `string` | `''` | space-separated list of objects to include in |
| `action` | | `'auto'` | |
| `quiet` | | `1` | |
**See also:** `ungroup`, `order`, `"group_auto_mode" setting`
### cmd.group\_sc
| Parameter | Type | Default | Description |
| --------- | ---- | ----------------------------------- | ----------- |
| `sc` | | `` | |
| `gnot` | | `` | |
### cmd.h\_add
"h\_add" adds hydrogens onto a molecule based on current valences.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
| `state` | | `0` | |
| `legacy` | | `0` | |
**See also:** `h_fill`
### cmd.h\_fill
"h\_fill" removes and replaces hydrogens on the atom or bond picked for editing.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
**See also:** `edit`, `cycle_valence`, `h_add`
### cmd.h\_fix
"h\_fix" is an unsupported command that may have something to do with repositioning hydrogen atoms.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | `''` | |
| `quiet` | | `1` | |
### cmd.help
"help" prints out the online help for a given command.
| Parameter | Type | Default | Description |
| --------- | ---- | ------------ | ----------- |
| `command` | | `'commands'` | |
### cmd.help\_setting
Print documentation for a setting.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `quiet` | | `1` | |
### cmd.hide
"hide" turns off atom and bond representations.
| Parameter | Type | Default | Description |
| ---------------- | -------- | -------------- | -------------------------------------- |
| `representation` | | `'everything'` | |
| `selection` | `string` | `''` | a selection-expression or name-pattern |
**See also:** `show`, `enable`, `disable`
### cmd.id\_atom
"id\_atom" returns the original source id of a single atom, or raises and exception if the atom does not exist or if the selection corresponds to multiple atoms.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
| `mode` | | `0` | |
| `quiet` | | `1` | |
### cmd.identify
"identify" returns a list of atom IDs corresponding to the ID code of atoms in the selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `mode` | | `0` | |
| `quiet` | | `1` | |
### cmd.index
"index" returns a list of tuples corresponding to the object name and index of the atoms in the selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
### cmd.indicate
"indicate" shows a visual representation of an atom selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
### cmd.interrupt
### cmd.intra\_fit
"intra\_fit" fits all states of an object to an atom selection in the specified state. It returns the rms values to python as an array.
| Parameter | Type | Default | Description |
| ----------- | --------- | ------- | --------------------------------------------------- |
| `selection` | `string` | | atoms to fit |
| `state` | `integer` | `1` | target state |
| `quiet` | | `1` | |
| `mix` | | `0` | |
| `pbc` | `0/1` | `1` | Consider periodic boundary conditions \{default: 1} |
**See also:** `fit`, `rms`, `rms_cur`, `intra_rms`, `intra_rms_cur`, `pair_fit`
### cmd.intra\_rms
"intra\_rms" calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
| `state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `fit`, `rms`, `rms_cur`, `intra_fit`, `intra_rms_cur`, `pair_fit`
### cmd.intra\_rms\_cur
"intra\_rms\_cur" calculates rms values for all states of an object over an atom selection relative to the indicated state without performing any fitting. The rms values are returned as a python array.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
| `state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `fit`, `rms`, `rms_cur`, `intra_fit`, `intra_rms`, `pair_fit`
### cmd.invert
"invert" inverts the stereo-chemistry of atom (pk1), holding attached atoms (pk2) and (pk3) immobile.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `1` | |
### cmd.ipython\_image
### cmd.is\_dict
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `obj` | | | |
### cmd.is\_error
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `result` | | | |
### cmd.is\_gui\_thread
### cmd.is\_list
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `obj` | | | |
### cmd.is\_ok
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `result` | | | |
### cmd.is\_sequence
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `obj` | | | |
### cmd.is\_string
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `obj` | | | |
### cmd.is\_tuple
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `obj` | | | |
### cmd.isodot
"isodot" creates a dot isosurface object from a map object.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `name` | | | |
| `map` | | | |
| `level` | | `1.0` | |
| `selection` | | `''` | |
| `buffer` | | `0.0` | |
| `state` | | `0` | |
| `carve` | | `None` | |
| `source_state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `load`, `isomesh`
### cmd.isolevel
"isolevel" changes the contour level of a isodot, isosurface, or isomesh object.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `level` | | `1.0` | |
| `state` | | `0` | |
| `query` | | `0` | |
| `quiet` | | `1` | |
### cmd.isomesh
"isomesh" creates a mesh isosurface object from a map object.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `name` | | | |
| `map` | | | |
| `level` | | `1.0` | |
| `selection` | | `''` | |
| `buffer` | | `0.0` | |
| `state` | | `1` | |
| `carve` | | `None` | |
| `source_state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `isodot`, `load`
### cmd.isosurface
"isosurface" creates a new surface object from a map object.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `name` | | | |
| `map` | | | |
| `level` | | `1.0` | |
| `selection` | | `''` | |
| `buffer` | | `0.0` | |
| `state` | | `1` | |
| `carve` | | `None` | |
| `source_state` | | `0` | |
| `side` | | `1` | |
| `mode` | | `3` | |
| `quiet` | | `1` | |
**See also:** `isodot`, `isomesh`, `load`
### cmd.iterate
"iterate" iterates over an expression within a temporary namespace for each atom.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `selection` | | | |
| `expression` | | `None` | |
| `quiet` | | `1` | |
| `space` | | `None` | |
**See also:** `iterate_state`, `alter`, `alter_state`
### cmd.iterate\_state
"iterate\_state" is to "alter\_state" as "iterate" is to "alter"
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `state` | | | |
| `selection` | | | |
| `expression` | | | |
| `quiet` | | `1` | |
| `space` | | `None` | |
| `atomic` | | `1` | |
**See also:** `iterate`, `alter`, `alter_state`
### cmd.join\_states
The reverse of split\_states. Create a multi-state object from a selection which spans multiple objects.
| Parameter | Type | Default | Description |
| ----------- | -------- | ------- | ---------------------------------- |
| `name` | `string` | | name of object to create or modify |
| `selection` | `string` | `'all'` | atoms to include in the new object |
| `mode` | `int` | `2` | how to match states \{default: 2} |
| `zoom` | | `0` | |
| `quiet` | | `1` | |
### cmd.label
"label" labels one or more atoms in a selection by evaluating an Python expression referencing properties for each atom.
| Parameter | Type | Default | Description |
| ------------ | -------- | --------- | ----------------------------------------------------- |
| `selection` | `string` | `'(all)'` | a selection-expression |
| `expression` | `string` | `''` | a Python expression that can be converted to a string |
| `quiet` | | `1` | |
### cmd.label2
| Parameter | Type | Default | Description |
| ------------ | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `expression` | | `''` | |
| `quiet` | | `1` | |
### cmd.load
"load" can by used to read molecules, crystallographic maps and other volumetric data, PyMOL sessions, and some other types of content.
| Parameter | Type | Default | Description |
| -------------- | --------- | ------- | ---------------------------------------------- |
| `filename` | `string` | | file path or URL |
| `object` | `string` | `''` | name of the object \{default: filename prefix} |
| `state` | `integer` | `0` | number of the state into which |
| `format` | | `''` | |
| `finish` | | `1` | |
| `discrete` | | `-1` | |
| `quiet` | | `1` | |
| `multiplex` | | `None` | |
| `zoom` | | `-1` | |
| `partial` | | `0` | |
| `mimic` | | `1` | |
| `object_props` | | `None` | |
| `atom_props` | | `None` | |
**See also:** `save`, `load_traj`, `fetch`
### cmd.load\_brick
### cmd.load\_callback
"load\_callback" is used to load a generic Python callback object. These objects are called every time the screen is updated and can be used to trigger OpenGL rendering calls (such as with PyOpenGL).
### cmd.load\_cgo
"load\_cgo" is used to load a compiled graphics object, which is actually a list of floating point numbers built using the constants in the \$PYMOL\_PATH/modules/pymol/cgo.py file.
### cmd.load\_coords
API only. Load selection coordinates. CHANGED IN VERSION 1.7.3: This used to be the load\_coordset function. load\_coordset may load coordinates in different order (original order from PDB file) than load\_coords (atom sorted order).
| Parameter | Type | Default | Description |
| ----------- | ------ | ------- | -------------------------- |
| `coords` | `list` | | Nx3 float array |
| `selection` | `str` | | atom selection |
| `state` | `int` | `1` | object state \{default: 1} |
| `quiet` | | `1` | |
### cmd.load\_coordset
API only. Load object coordinates. Loads them in the original atom order (order from PDB file for example), not in the atom property sorted order (like cmd.iterate, cmd.load\_coods, etc.).
| Parameter | Type | Default | Description |
| --------- | ------ | ------- | ------------------------------------------- |
| `coords` | `list` | | Nx3 float array |
| `object` | `str` | | object name |
| `state` | `int` | `0` | object state, or 0 for append \{default: 0} |
| `quiet` | | `1` | |
**See also:** `cmd.load_coords`
### cmd.load\_embedded
"load\_embedded" loads content previously defined in the current PyMOL command script using the "embed" command.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `key` | | `None` | |
| `name` | | `None` | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `1` | |
| `quiet` | | `1` | |
| `zoom` | | `-1` | |
| `multiplex` | | `-2` | |
| `object_props` | | `None` | |
| `atom_props` | | `None` | |
### cmd.load\_map
### cmd.load\_model
"load\_model" reads a ChemPy model into an object
### cmd.load\_mtz
Load a MTZ file as two map objects (fofc, 2fofc) or if amplitudes and phases column names are given, as one map object.
| Parameter | Type | Default | Description |
| ------------ | ------- | -------- | ----------------------------------------------------------------- |
| `filename` | `str` | | filename |
| `prefix` | `str` | `''` | object name or prefix \{default: filename without extension} |
| `amplitudes` | `str` | `''` | amplitudes column name, guess if blank \{default: } |
| `phases` | `str` | `''` | phases column name, required if amplitudes are given \{default: } |
| `weights` | `str` | `'None'` | weights column name, optional \{default: None} |
| `reso_low` | `float` | `0` | minimum resolution \{default: 0, read from file} |
| `reso_high` | `float` | `0` | maximum resolution \{default: 0, read from file} |
| `quiet` | | `1` | |
### cmd.load\_object
"load\_object" is a general developer function for loading Python objects into PyMOL.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `type` | | | |
| `object` | | | |
| `name` | | | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `0` | |
| `quiet` | | `1` | |
| `zoom` | | `-1` | |
### cmd.load\_png
"load\_png" loads and displays a PNG file from disk.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `filename` | | | |
| `movie` | | `1` | |
| `stereo` | | `-1` | |
| `quiet` | | `0` | |
### cmd.load\_raw
API-only function for loading data from memory.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `content` | | | |
| `format` | | | |
| `object` | | `''` | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `-1` | |
| `quiet` | | `1` | |
| `multiplex` | | `None` | |
| `zoom` | | `-1` | |
### cmd.load\_traj
"load\_traj" reads trajectory files. Most of the trajectory formats listed here are supported: [http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/](http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/)
| Parameter | Type | Default | Description |
| ----------- | ----- | ----------------- | ---------------------------------------------------------------- |
| `filename` | `str` | | path to trajectory file |
| `object` | `str` | `''` | name of the molecular object where the trajectory should be |
| `state` | `int` | `1` | first object state to populate, or 0 to append after |
| `format` | `str` | `''` | file format \{default: guess from extension} |
| `interval` | `int` | `1` | interval to take frames from file \{default: 1} |
| `average` | `int` | `1` | ? (trj only, possibly broken) |
| `start` | `int` | `1` | first frame to load from file \{default: 1} |
| `stop` | `int` | `-1` | last frame to load from file, or -1 to load all \{default: -1} |
| `max` | `int` | `-1` | maximum number of states to load, or 0 to load all \{default: 0} |
| `selection` | `str` | `'all'` | atom selection to only load a subset of coordinates |
| `image` | `0/1` | `1` | residue-based period image transformation (trj only) |
| `shift` | | `'[0.0,0.0,0.0]'` | |
| `plugin` | `str` | `''` | name of VMD plugin to use \{default: guess from magic string |
**See also:** `load`
### cmd.loadable
### cmd.loadall
Load all files matching given globbing pattern
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `pattern` | | | |
| `group` | | `''` | |
| `quiet` | | `1` | |
### cmd.lock
### cmd.lock\_attempt
### cmd.lock\_without\_glut
### cmd.log
"log" writes a command to the log file (if one is open). `text` and/or `alt_text` must include the terminating line feed.
| Parameter | Type | Default | Description |
| ---------- | ----- | ------- | ---------------------------------------------- |
| `text` | `str` | | PyMOL command (optional if alt\_text is given) |
| `alt_text` | `str` | `None` | Python expression (optional) |
**See also:** `log_open`, `log_close`
### cmd.log\_close
"log\_close" closes the current log file (if one is open).
**See also:** `log`, `log_open`
### cmd.log\_open
"log\_open" opens a log file for writing.
| Parameter | Type | Default | Description |
| ---------- | ----- | ----------- | ---------------------------------------------------------- |
| `filename` | `str` | `'log.pml'` | file to write to (.pml or .py) \{default: log.pml} |
| `mode` | `w/a` | `'w'` | "w" to open an empty log file, "a" to append \{default: w} |
**See also:** `log`, `log_close`
### cmd.look\_at
"look\_at" modifies a rotation of an object (or view) so that its forward (z axis) faces the center of a target object.
| Parameter | Type | Default | Description |
| ------------ | ----- | ----------- | ----------- |
| `target_obj` | `str` | | |
| `mobile_obj` | `str` | `'_Camera'` | |
### cmd.ls
List contents of the current working directory.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `pattern` | | `None` | |
**See also:** `cd`, `pwd`, `system`
### cmd.madd
"madd" extends the existing movie specification using the same syntax as mset.
| Parameter | Type | Default | Description |
| --------------- | ---- | ------- | ----------- |
| `specification` | | `''` | |
| `frame` | | `0` | |
| `freeze` | | `0` | |
**See also:** `mset`, `mdo`, `mplay`, `mclear`
### cmd.map\_double
"map\_double" resamples a map at twice the current resolution.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `state` | | `0` | |
### cmd.map\_generate
"map\_generate" generates a map object from a PDB object or selection and reflection data. Experimental use with caution.
| Parameter | Type | Default | Description |
| ----------------- | -------- | -------- | --------------------------------------------------- |
| `name` | `string` | | name of the map object to create or modify |
| `reflection_file` | `string` | | name of reflection file on disk; if None, then |
| `amplitudes` | `string` | | fully qualified apmlitudes column name. Properly |
| `phases` | `string` | | fully qualified phases column name. Properly |
| `weights` | `string` | `'None'` | fully qualified phases column name. Properly |
| `reso_low` | `float` | `50.0` | minimum resolution; if set to equal max\_reso, then |
| `reso_high` | `float` | `1.0` | maximum resolution; if set to equal min\_reso then |
| `quiet` | | `1` | |
| `zoom` | | `1` | |
### cmd.map\_halve
"map\_halve" resamples a map at half the current resolution.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `state` | | `0` | |
| `smooth` | | `1` | |
**See also:** `map_double`
### cmd.map\_new
"map\_new" creates a map object using one of the built-in map generation routines. This command not yet fully supported.
| Parameter | Type | Default | Description |
| ------------ | -------- | ------------- | ----------------------------------------------------- |
| `name` | `string` | | name of the map object to create or modify |
| `type` | | `'gaussian'` | |
| `grid` | `float` | `None` | grid spacing |
| `selection` | `string` | `'(all)'` | atoms about which to generate the map |
| `buffer` | `float` | `None` | cutoff |
| `box` | | `None` | |
| `state` | `0` | `0` | use all states independently with independent extents |
| `quiet` | | `1` | |
| `zoom` | | `0` | |
| `normalize` | | `-1` | |
| `clamp` | | `[1.0, -1.0]` | |
| `resolution` | | `0.0` | |
### cmd.map\_sc
| Parameter | Type | Default | Description |
| --------- | ---- | ----------------------------------- | ----------- |
| `sc` | | `` | |
| `gnot` | | `` | |
### cmd.map\_set
"map\_set" provides a number of common operations on and between maps.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `name` | | | |
| `operator` | | | |
| `operands` | | `''` | |
| `target_state` | | `0` | |
| `source_state` | | `0` | |
| `zoom` | | `0` | |
| `quiet` | | `1` | |
**See also:** `map_new`
### cmd.map\_set\_border
"map\_set\_border" is a function (reqd by PDA) which allows you to set the level on the edge points of a map
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `level` | | `0.0` | |
| `state` | | `0` | |
**See also:** `load`
### cmd.map\_trim
"map\_trim" is an unsupported command that may have something to do with reducing the extent of a map to cover just a single selection of atoms.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `name` | | | |
| `selection` | | | |
| `buffer` | | `0.0` | |
| `map_state` | | `0` | |
| `sele_state` | | `0` | |
| `quiet` | | `1` | |
### cmd.mappend
"mappend" associates additional command line operations with a particular movie frame. These "generalized movie commands" will be executed every time the numbered frame is played.
| Parameter | Type | Default | Description |
| --------- | --------- | ------- | ------------------- |
| `frame` | `integer` | | the frame to modify |
| `command` | | | |
**See also:** `mset`, `madd`, `mdo`, `mplay`, `mstop`
### cmd.mask
"mask" makes it impossible to select the indicated atoms using the mouse. This is useful when you are working with one molecule in front of another and wish to avoid accidentally selecting atoms in the background.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
**See also:** `unmask`, `protect`, `deprotect`, `mouse`
### cmd.matrix\_copy
"matrix\_copy" copies a transformation matrix from one object to another.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `source_name` | | `''` | |
| `target_name` | | `''` | |
| `source_mode` | | `-1` | |
| `target_mode` | | `-1` | |
| `source_state` | | `1` | |
| `target_state` | | `1` | |
| `target_undo` | | `1` | |
| `log` | | `0` | |
| `quiet` | | `1` | |
**See also:** `matrix_reset`, `align`, `fit`, `pair_fit`
### cmd.matrix\_reset
"matrix\_reset" resets the transformation for an object.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ---------------------------------- |
| `name` | `str` | | object name |
| `state` | `int` | `1` | object state \{default: 1} |
| `mode` | `int` | `-1` | \{defualt: -1 = matrix\_mode or 0} |
| `log` | | `0` | |
| `quiet` | | `1` | |
**See also:** `matrix_copy`, `align`, `super`, `fit`, `pair_fit`
### cmd.matrix\_transfer
"matrix\_copy" copies a transformation matrix from one object to another.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `source_name` | | `''` | |
| `target_name` | | `''` | |
| `source_mode` | | `-1` | |
| `target_mode` | | `-1` | |
| `source_state` | | `1` | |
| `target_state` | | `1` | |
| `target_undo` | | `1` | |
| `log` | | `0` | |
| `quiet` | | `1` | |
**See also:** `matrix_reset`, `align`, `fit`, `pair_fit`
### cmd.mclear
"mclear" clears the movie frame image cache.
### cmd.mcopy
"mcopy" copies key frames and movie commands Usage like "mmove".
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `target` | | | |
| `source` | | `0` | |
| `count` | | `-1` | |
| `freeze` | | `0` | |
| `object` | | `''` | |
| `quiet` | | `1` | |
**See also:** `mmove`, `mdelete`, `minsert`
### cmd.mdelete
"mdelete" removes frames from camera view and object motions.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ----------------------------------------------------------- |
| `count` | `int` | `-1` | number of frames to delete, or -1 to delete all the way |
| `frame` | `int` | `0` | first frame to delete, or 0 for current frame \{default: 0} |
| `freeze` | | `0` | |
| `object` | | `''` | |
| `quiet` | | `1` | |
**See also:** `minsert`, `mmove`
### cmd.mdo
"mdo" defines (or redefines) the command-line operations associated with a particular movie frame. These "generalized movie commands" will be executed every time the numbered frame is played.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `frame` | | | |
| `command` | | | |
**See also:** `mset`, `mplay`, `mstop`
### cmd.mdump
"mdump" dumps the current set of movie commands as text output.
**See also:** `mplay`, `mset`, `mdo`, `mclear`, `mmatrix`
### cmd.mem
"mem" Dumps current memory state to standard output. This is a debugging feature, not an official part of the API.
### cmd.meter\_reset
"meter\_reset" resets the frames per secound counter.
### cmd.middle
"middle" goes to the middle of the movie.
### cmd.minimize
"fast\_minimize" is an unsupported nonfunctional command that may eventually have something to do with minimization.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `sele` | | `''` | |
| `iter` | | `500` | |
| `grad` | | `0.01` | |
| `interval` | | `50` | |
| `_setup` | | `1` | |
### cmd.minsert
"minsert" adds frames into camera view and object motions.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ----------------------------------------------------------- |
| `count` | `int` | | number of frames to insert |
| `frame` | `int` | `0` | insert before "frame" if frame > 0, otherwise insert before |
| `freeze` | | `0` | |
| `object` | | `''` | |
| `quiet` | | `1` | |
**See also:** `mdelete`, `mmove`, `madd`
### cmd.mmatrix
"mmatrix" sets up a matrix to be used for the first frame of the movie.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `action` | | | |
### cmd.mmove
"mmove" moves key frames and movie commands
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ----------------------------------------------------- |
| `target` | `int` | | frame to move to |
| `source` | `int` | `0` | frame to move from, 0 for current frame \{default: 0} |
| `count` | `int` | `-1` | number of frames to move |
| `freeze` | | `0` | |
| `object` | | `''` | |
| `quiet` | | `1` | |
**See also:** `mcopy`, `mdelete`, `minsert`
### cmd.morph
Creates an interpolated trajectory between two or multiple conformations. If the two input objects are not the same, match them based on sequence alignment. This command supports two methods: rigimol and linear. RigiMOL is an incentive feature and only available to official PyMOL sponsors. Linear morphing is quick and robust but likely to produce distorted intermediates.
| Parameter | Type | Default | Description |
| ------------ | -------- | ----------- | ---------------------------------------------------------- |
| `name` | `string` | | name of object to create |
| `sele1` | `string` | | atom selection of first conformation |
| `sele2` | `string` | `None` | atom selection of second conformation \{default: \} |
| `state1` | `int` | `-1` | sele1 state \{default: 1}. If state1=0 and sele1 has N |
| `state2` | `int` | `-1` | sele2 state \{default: 2 if sele1=sele2, else 1} |
| `refinement` | `int` | `3` | number of sculpting refinement cycles to clean |
| `steps` | `int` | `30` | number of states for sele2 object \{default: 30} |
| `method` | `string` | `'rigimol'` | rigimol or linear \{default: rigimol} |
| `match` | | `'align'` | |
| `quiet` | | `1` | |
### cmd.mouse
"mouse" cycles through the mouse modes defined in the current mouse configuration ring.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `action` | | `None` | |
| `quiet` | | `1` | |
### cmd.move
"move" translates the camera about one of the three primary axes.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `axis` | | | |
| `distance` | | | |
**See also:** `turn`, `rotate`, `translate`, `zoom`, `center`, `clip`
### cmd.move\_on\_curve
"move\_on\_curve" moves an object along a curve.
| Parameter | Type | Default | Description |
| ------------ | ------- | ------- | ----------- |
| `mobile_obj` | `str` | | |
| `curve_obj` | `str` | | |
| `t` | `float` | | |
### cmd.mplay
"mplay" starts the movie.
**See also:** `mstop`, `mset`, `mdo`, `mclear`, `mmatrix`
### cmd.mpng
"mpng" writes movie frames as a series of numbered png files.
| Parameter | Type | Default | Description |
| ---------- | --------- | ------- | ------------------------------------------------ |
| `prefix` | `string` | | filename prefix for saved images -- output files |
| `first` | `integer` | `0` | starting frame \{default: 0 (first frame)} |
| `last` | `integer` | `0` | last frame \{default: 0 (last frame)} |
| `preserve` | `0/1` | `0` | Only write non-existing files \{default: 0} |
| `modal` | `integer` | `0` | will frames be rendered with a modal draw loop |
| `mode` | `int` | `-1` | 2=ray, 1=draw, 0=normal \{default: -1, check |
| `quiet` | | `1` | |
| `width` | `int` | `0` | width in pixels \{default: current viewport} |
| `height` | `int` | `0` | height in pixels \{default: current viewport} |
**See also:** `png`, `save`
### cmd.mse2met
Mutate selenomethionine to methionine
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | `'all'` | |
| `quiet` | | `1` | |
### cmd.mset
"mset" sets up a relationship between molecular states and movie frames. This makes it possible to control which states are shown in which frame.
| Parameter | Type | Default | Description |
| --------------- | ---- | ------- | ----------- |
| `specification` | | `''` | |
| `frame` | | `1` | |
| `freeze` | | `0` | |
**See also:** `madd`, `mdo`, `mplay`, `mclear`
### cmd.mstop
"mstop" stops playing of the movie.
**See also:** `mplay`, `mset`, `mdo`, `mclear`, `mmatrix`
### cmd.mtoggle
"mtoggle" toggles playing of the movie.
### cmd.multifilenamegen
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `filename` | | | |
| `selection` | | | |
| `state` | | | |
### cmd.multifilesave
For a selection that spans multiple molecular objects and/or states, save each object and/or state to a separate file. Takes a filename argument with placeholders: \{name} : object name \{state} : state number \{title} : state title \{num} : file number \{} : object name (first) or state (second)
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `filename` | | | |
| `selection` | | `'*'` | |
| `state` | | `-1` | |
| `format` | | `''` | |
| `ref` | | `''` | |
| `ref_state` | | `-1` | |
| `quiet` | | `1` | |
### cmd.multisave
"multisave" will save a multi-entry PDB file. Every object in the given selection (pattern) will have a HEADER and a CRYST (if symmetry is defined) record, and is terminated with END. Loading such a multi-entry PDB file into PyMOL will load each entry as a separate object. This behavior is different to the "save" command, where a multi-object selection is written "flat" to a PDB file, without HEADER or CRYST records.
| Parameter | Type | Default | Description |
| ---------- | -------- | ------- | ------------------------------------------------------ |
| `filename` | `string` | | file path to be written |
| `pattern` | `str` | `'all'` | atom selection (before 1.8.4: object name pattern) |
| `state` | `int` | `-1` | object state (-1=current, 0=all) \{default: -1} |
| `append` | `0/1` | `0` | append to existing file \{default: 0} |
| `format` | `str` | `''` | file format \{default: guess from extension, or 'pdb'} |
| `quiet` | | `1` | |
### cmd.mview
"mview" stores camera and object matrices for use in movie interpolation.
| Parameter | Type | Default | Description |
| --------- | ------- | --------- | -------------------------------------------------------- |
| `action` | `str` | `'store'` | one of store, clear, reset, purge, interpolate, |
| `first` | `int` | `0` | frame number or 0 for current frame \{default: 0} |
| `last` | | `0` | |
| `power` | `float` | `0.0` | slow down animation at keyframe (0.0) or not (1.0) |
| `bias` | | `-1.0` | |
| `simple` | | `-1` | |
| `linear` | | `0.0` | |
| `object` | `str` | `''` | name of object for object keyframes, or empty for |
| `wrap` | | `-1` | |
| `hand` | | `0` | |
| `window` | | `5` | |
| `cycles` | | `1` | |
| `scene` | `str` | `''` | name of scene to store scene with key frame \{default: } |
| `cut` | | `0.5` | |
| `quiet` | | `1` | |
| `auto` | | `-1` | |
| `state` | `int` | `0` | if > 0, then store object state \{default: 0} |
| `freeze` | `0/1` | `0` | never auto reinterpolate \{default: 0} |
**See also:** `mplay`, `mset`, `mdo`, `mclear`, `mmatrix`
### cmd.object\_sc
| Parameter | Type | Default | Description |
| --------- | ---- | ----------------------------------- | ----------- |
| `sc` | | `` | |
| `gn` | | `` | |
### cmd.order
"order" changes the ordering of names in the control panel.
| Parameter | Type | Default | Description |
| ---------- | -------- | ----------- | ------------------------------- |
| `names` | `string` | | a space-separated list of names |
| `sort` | | `0` | |
| `location` | | `'current'` | |
**See also:** `set_name`, `group`
### cmd.orient
"orient" aligns the principal components of the atoms in the selection with the XYZ axes.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ------------------------------------ |
| `selection` | | `'(all)'` | |
| `state` | `0` | `0` | use all coordinate states \{default} |
| `animate` | | `0` | |
**See also:** `zoom`, `origin`, `reset`
### cmd.origin
"origin" sets the center of rotation about a selection. If an object name is specified, it can be used to set the center of rotation for the object (for use in animation and editing).
| Parameter | Type | Default | Description |
| ----------- | -------- | --------- | --------------------------------------------------- |
| `selection` | `string` | `'(all)'` | selection-expression or name-list \{default: (all)} |
| `object` | | `None` | |
| `position` | | `None` | |
| `state` | | `0` | |
**See also:** `zoom`, `orient`, `reset`
### cmd.overlap
"overlap" is an unsupported command that sums up \[(VDWi + VDWj) - distance\_ij]/2 between pairs of selected atoms.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `selection1` | | | |
| `selection2` | | | |
| `state1` | | `1` | |
| `state2` | | `1` | |
| `adjust` | | `0.0` | |
| `quiet` | | `1` | |
### cmd.pair\_fit
"pair\_fit" fits matched sets of atom pairs between two objects.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `quiet` | | `0` | |
**See also:** `fit`, `rms`, `rms_cur`, `intra_fit`, `intra_rms`, `intra_rms_cur`
### cmd.paste
### cmd.pbc\_unwrap
Unwrap molecules or atoms from PBC box so that they don't jump across periodic boundaries.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | --------------------------------------------- |
| `oname` | `str` | | object name |
| `bymol` | `0/1` | `True` | Unwrap by molecule, not by atom \{default: 1} |
### cmd.pbc\_wrap
Wrap molecules into PBC box.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ----------- |
| `oname` | `str` | | object name |
| `center` | | `None` | |
### cmd.phi\_psi
"phi\_psi" return the phi and psi angles for a protein atom selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------------- | ----------- |
| `selection` | | `'(byres pk1)'` | |
| `quiet` | | `1` | |
### cmd.pi\_interactions
Find pi-pi and pi-cation interactions. Identical to cmd.distance(..., mode=5, label=0)
| Parameter | Type | Default | Description |
| ------------ | ---- | -------- | ----------- |
| `name` | | `''` | |
| `selection1` | | `'all'` | |
| `selection2` | | `'same'` | |
| `state` | | `0` | |
| `state1` | | `-3` | |
| `state2` | | `-3` | |
| `quiet` | | `1` | |
| `reset` | | `0` | |
**See also:** `distance`
### cmd.png
"png" saves a PNG format image file of the current display.
| Parameter | Type | Default | Description |
| ---------- | -------- | ------- | ------------------------------------------- |
| `filename` | `string` | | file path to be written |
| `width` | | `0` | |
| `height` | | `0` | |
| `dpi` | `float` | `-1.0` | dots-per-inch \{default -1.0 (unspecified)} |
| `ray` | | `0` | |
| `quiet` | | `1` | |
| `prior` | | `0` | |
| `format` | | `0` | |
**See also:** `mpng`, `save`
### cmd.pop
"pop" provides a mechanism of iterating through an atom selection atom by atom, where each atom is sequentially assigned to the named selection.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `source` | | | |
| `enable` | | `-1` | |
| `quiet` | | `1` | |
### cmd.pretty
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `solv` | | `False` | |
### cmd.protect
"protect" protects a set of atoms from tranformations performed using the editing features. This is most useful when you are modifying an internal portion of a chain or cycle and do not wish to affect the rest of the molecule.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
**See also:** `deprotect`, `mask`, `unmask`, `mouse`, `editing`
### cmd.protonate
"protonate" adds hydrogens with pH-dependent protonation states. When pdb2pqr is available, uses PROPKA for per-residue pKa prediction. Otherwise, falls back to textbook pKa values for standard titratable residues. Unlike "h\_add" which fills all open valences, "protonate" considers pKa values to determine which atoms should be protonated at the given pH. Heavy atoms and their visual settings (colors, representations) are
| Parameter | Type | Default | Description |
| ----------- | -------- | --------- | ----------------------------------------------------------------- |
| `selection` | | `'all'` | |
| `pH` | `float` | `7.4` | target pH for protonation \{default: 7.4} |
| `ff` | `string` | `'amber'` | pdb2pqr forcefield (amber, charmm, parse, etc.) \{default: amber} |
| `state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `h_add`, `h_fill`
### cmd.pseudoatom
"pseudoatom" adds a pseudoatom to a molecular object, and will creating the molecular object if it does not yet exist.
| Parameter | Type | Default | Description |
| ----------- | ---- | -------- | ----------- |
| `object` | | `''` | |
| `selection` | | `''` | |
| `name` | | `'PS1'` | |
| `resn` | | `'PSD'` | |
| `resi` | | `'1'` | |
| `chain` | | `'P'` | |
| `segi` | | `'PSDO'` | |
| `elem` | | `'PS'` | |
| `vdw` | | `-1.0` | |
| `hetatm` | | `1` | |
| `b` | | `0.0` | |
| `q` | | `0.0` | |
| `color` | | `''` | |
| `label` | | `''` | |
| `pos` | | `None` | |
| `state` | | `0` | |
| `mode` | | `'rms'` | |
| `quiet` | | `1` | |
### cmd.publication
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `solv` | | `False` | |
### cmd.push\_undo
"push\_undo" stores the current conformations of objects in the selection onto their individual undo rings. Notice: This command is only partly implemented in open-source PyMOL.
| Parameter | Type | Default | Description |
| ------------------ | ---- | ------- | ----------- |
| `selection` | | | |
| `just_coordinates` | | `1` | |
| `finish_undo` | | `0` | |
| `add_objects` | | `0` | |
| `delete_objects` | | `0` | |
| `state` | | `0` | |
**See also:** `undo`, `redo`
### cmd.pwd
Print current working directory.
**See also:** `cd`, `ls`, `system`
### cmd.python\_help
You have asked for help on a Python keyword which is available from within the PyMOL command language. Please consult the official Python documentation at [http://www.python.org](http://www.python.org) for detailed information on Python keywords. You may include Python blocks in your PyMOL command scripts, but do note that multi-line blocks of Python in PyMOL command files will require explicit continuation syntax in order to execute properly (see below).
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `string` | | | |
**See also:** `extend`, `run`, `@`
### cmd.ramp\_new
"ramp\_new" creates a color ramp based on a map potential value or based on proximity to a molecular object.
| Parameter | Type | Default | Description |
| ----------- | ----------- | ---------------------------------- | ----------------------------------------------- |
| `name` | `string` | | name of the ramp object |
| `map_name` | `string` | | name of the map (for potential) or molecular |
| `range` | `list` | `[-1.0, 0.0, 1.0]` | values corresponding to slots in the ramp |
| `color` | `list` | `['red', [1.0, 1.0, 1.0], 'blue']` | colors corresponding to slots in the ramp |
| `state` | `integer` | `1` | state identifier |
| `selection` | `selection` | `''` | for automatic ranging |
| `beyond` | `number` | `2.0` | with automatic ranging, are we excluding |
| `within` | `number` | `6.0` | with automatic ranging, are we only including |
| `sigma` | `number` | `2.0` | with automatic ranging, how many standard |
| `zero` | `integer` | `1` | with automatic ranging, do we force the central |
| `quiet` | | `1` | |
**See also:** `ramp_update`, `load`, `color`, `create`, `slice`, `gradient`
### cmd.ramp\_update
"ramp\_update" updates range and/or color of a color ramp.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `range` | | `[]` | |
| `color` | | `[]` | |
| `quiet` | | `1` | |
**See also:** `ramp_new`
### cmd.ray
"ray" creates a ray-traced image of the current frame. This can take some time (up to several minutes, depending on image complexity).
| Parameter | Type | Default | Description |
| ----------- | ------- | ------- | ---------------------------------------------- |
| `width` | | `0` | |
| `height` | | `0` | |
| `antialias` | | `-1` | |
| `angle` | `float` | `0.0` | y-axis rotation for stereo image generation |
| `shift` | `float` | `0.0` | x-axis translation for stereo image generation |
| `renderer` | | `-1` | |
| `quiet` | | `1` | |
| `async_` | | `0` | |
**See also:** `draw`, `png`, `save`
### cmd.read\_mmodstr
"read\_mmodstr" reads a macromodel format structure from a Python string.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `content` | | | |
| `name` | | | |
| `state` | | `0` | |
| `quiet` | | `1` | |
| `zoom` | | `-1` | |
### cmd.read\_molstr
"read\_molstr" reads an MDL MOL format file as a string
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `molstr` | | | |
| `name` | | | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `1` | |
| `quiet` | | `1` | |
| `zoom` | | `-1` | |
### cmd.read\_pdbstr
"read\_pdbstr" in an API-only function which reads a pdb file from a Python string. This feature can be used to load or update structures into PyMOL without involving any temporary files.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `contents` | | | |
| `oname` | | | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `0` | |
| `quiet` | | `1` | |
| `zoom` | | `-1` | |
| `multiplex` | | `-2` | |
| `object_props` | | `None` | |
### cmd.read\_sdfstr
"read\_sdfstr" reads an MDL MOL format file as a string
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `sdfstr` | | | |
| `name` | | | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `1` | |
| `quiet` | | `1` | |
| `zoom` | | `-1` | |
| `multiplex` | | `-2` | |
| `object_props` | | `None` | |
### cmd.read\_xplorstr
"read\_xplorstr" in an API-only function which reads an XPLOR map from a Python string. This feature can be used to bypass temporary files.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `xplor` | | | |
| `name` | | | |
| `state` | | `0` | |
| `finish` | | `1` | |
| `discrete` | | `0` | |
| `quiet` | | `1` | |
| `zoom` | | `-1` | |
### cmd.ready
### cmd.rebond
Discard all bonds and do distance based bonding.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | -------------------------------------------------- |
| `oname` | `str` | | object name |
| `state` | `int` | `-1` | object state \{default: -1 (current state)} |
| `pbc` | `0/1` | `1` | Use periodic boundary conditions (only if symmetry |
### cmd.rebuild
"rebuild" forces PyMOL to recreate geometric objects in case any of them have gone out of sync.
| Parameter | Type | Default | Description |
| ---------------- | -------- | -------------- | ---------------------- |
| `selection` | | `'all'` | |
| `representation` | `string` | `'everything'` | \{default: everything} |
**See also:** `refresh`
### cmd.recolor
"recolor" forces reapplication of colors to existing objects.
| Parameter | Type | Default | Description |
| ---------------- | ---- | -------------- | ----------- |
| `selection` | | `'all'` | |
| `representation` | | `'everything'` | |
**See also:** `color`, `set_color`
### cmd.recolour
"recolor" forces reapplication of colors to existing objects.
| Parameter | Type | Default | Description |
| ---------------- | ---- | -------------- | ----------- |
| `selection` | | `'all'` | |
| `representation` | | `'everything'` | |
**See also:** `color`, `set_color`
### cmd.redo
"redo" reapplies the conformational change of the object currently being edited.
**See also:** `undo`, `push_undo`
### cmd.reference
| Parameter | Type | Default | Description |
| ----------- | ---- | ------------ | ----------- |
| `action` | | `'validate'` | |
| `selection` | | `'(all)'` | |
| `state` | | `0` | |
| `quiet` | | `1` | |
### cmd.refresh
"refresh" causes the scene to be redrawn as soon as the operating system allows it to be done.
**See also:** `rebuild`
### cmd.refresh\_wizard
"refresh\_wizard" is in unsupported internal command.
### cmd.reinitialize
"reinitialize" reinitializes the program by deleting all objects and restoring the default program settings.
| Parameter | Type | Default | Description |
| --------- | ---- | -------------- | ----------- |
| `what` | | `'everything'` | |
| `object` | | `''` | |
### cmd.remove
"remove" eleminates the atoms in a selection from their respective molecular objects.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
| `quiet` | | `1` | |
**See also:** `delete`
### cmd.remove\_picked
"remove\_picked" removes the atom or bond currently picked for editing.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `hydrogens` | | `1` | |
| `quiet` | | `1` | |
**See also:** `attach`, `replace`
### cmd.rename
"rename" creates new atom names which are unique within residues.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | `'all'` | |
| `force` | | `0` | |
| `quiet` | | `1` | |
**See also:** `alter`
### cmd.replace
"replace" replaces the picked atom with a new atom.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `element` | | | |
| `geometry` | | | |
| `valence` | | | |
| `h_fill` | | `1` | |
| `name` | | `''` | |
| `quiet` | | `1` | |
**See also:** `remove`, `attach`, `fuse`, `bond`, `unbond`
### cmd.replace\_wizard
"replace\_wizard" is an unsupported internal command.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | `None` | |
### cmd.reset
"reset" restores the rotation matrix to identity, sets the origin to the center of mass (approx.) and zooms the window and clipping planes to cover all objects. Alternatively, it can reset object matrices.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | `''` | |
### cmd.resume
"resume" executes a log file and opens it for recording of additional commands.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `filename` | | | |
**See also:** `log`, `log_close`
### cmd.rewind
"rewind" goes to the beginning of the movie.
### cmd.rms
"rms" computes a RMS fit between two atom selections, but does not tranform the models after performing the fit.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `mobile` | | | |
| `target` | | | |
| `mobile_state` | | `0` | |
| `target_state` | | `0` | |
| `quiet` | | `1` | |
| `matchmaker` | | `0` | |
| `cutoff` | | `2.0` | |
| `cycles` | | `0` | |
| `object` | | `None` | |
**See also:** `fit`, `rms_cur`, `intra_fit`, `intra_rms`, `intra_rms_cur`, `pair_fit`
### cmd.rms\_cur
"rms\_cur" computes the RMS difference between two atom selections without performing any fitting.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `mobile` | | | |
| `target` | | | |
| `mobile_state` | | `0` | |
| `target_state` | | `0` | |
| `quiet` | | `1` | |
| `matchmaker` | | `0` | |
| `cutoff` | | `2.0` | |
| `cycles` | | `0` | |
| `object` | | `None` | |
**See also:** `fit`, `rms`, `intra_fit`, `intra_rms`, `intra_rms_cur`, `pair_fit`
### cmd.rock
"rock" toggles Y axis rocking.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `mode` | | `-1` | |
### cmd.rotate
"rotate" rotates the atomic coordinates of atoms in a selection about an axis. Alternatively, it modifies the matrix associated with a particular object or object state.
| Parameter | Type | Default | Description |
| ------------- | -------- | ------- | ------------------------------------------------------------- |
| `axis` | | `'x'` | |
| `angle` | `float` | `0.0` | degrees of rotation |
| `selection` | `string` | `'all'` | atoms whose coordinates should be modified \{default: all} |
| `state` | `0` | `-1` | all states are modified |
| `camera` | | `1` | |
| `object` | `string` | `None` | object name (only if rotating object matrix) \{default: None} |
| `origin` | | `None` | |
| `object_mode` | | `0` | |
### cmd.safe\_alpha\_list\_eval
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `st` | | | |
### cmd.safe\_eval
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `st` | | | |
### cmd.safe\_list\_eval
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `st` | | | |
### cmd.save
"save" writes content to a file.
| Parameter | Type | Default | Description |
| ----------- | --------- | --------- | -------------------------------------------- |
| `filename` | `string` | | file path to be written |
| `selection` | `string` | `'(all)'` | atoms to save \{default: (all)} |
| `state` | `integer` | `-1` | state to save \{default: -1 (current state)} |
| `format` | | `''` | |
| `ref` | | `''` | |
| `ref_state` | | `-1` | |
| `quiet` | | `1` | |
| `partial` | | `0` | |
**See also:** `load`, `get_model`
### cmd.scene
"scene" saves and restores scenes. A scene consists of the camera view, all object activity information, all atom-wise visibilities, all atom-wise colors, all representations, the global frame index, and may contain a text message to display on playback.
| Parameter | Type | Default | Description |
| --------- | -------- | ---------- | ----------------------------------------- |
| `key` | | `'auto'` | |
| `action` | | `'recall'` | |
| `message` | `string` | `None` | a text message to display with the scene. |
| `view` | | `1` | |
| `color` | | `1` | |
| `active` | | `1` | |
| `rep` | | `1` | |
| `frame` | | `1` | |
| `animate` | | `-1` | |
| `new_key` | `string` | `None` | the new name for the scene |
| `hand` | | `1` | |
| `quiet` | | `1` | |
| `sele` | | `'all'` | |
**See also:** `view`, `set_view`, `get_view`
### cmd.scene\_order
"scene\_order" changes the ordering of scenes.
| Parameter | Type | Default | Description |
| ---------- | -------- | ----------- | ------------------------------- |
| `names` | `string` | | a space-separated list of names |
| `sort` | | `0` | |
| `location` | | `'current'` | |
| `quiet` | | `1` | |
**See also:** `scene`
### cmd.scene\_recall\_message
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `message` | | | |
### cmd.sculpt\_activate
"sculpt\_activate" enables sculpting for the given object. The current geometry (bond lengths, angles, etc.) of the given state is remembered as the reference geometry.
| Parameter | Type | Default | Description |
| ------------------ | ----- | ------- | ------------------------------------------------- |
| `object` | `str` | | name of a single object or "all" |
| `state` | `int` | `0` | object state or 0 for current state \{default: 0} |
| `match_state` | | `-1` | |
| `match_by_segment` | | `0` | |
**See also:** `sculpt_iterate`, `sculpt_deactivate`
### cmd.sculpt\_deactivate
"sculpt\_deactivate" deactivates sculpting for the given object and clears the stored restraints.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | -------------------------------- |
| `object` | `str` | | name of a single object or "all" |
**See also:** `sculpt_activate`
### cmd.sculpt\_iterate
"sculpt\_iterate" performs a simple energy minimization of atomic coordinates based on the geometry restraints which were defined with the "sculpt\_activate" invocation and which are selected in the "sculpt\_field\_mask" setting. Sculpting currently supports local geometry restraints and vdw repulsion, but no solvation or electrostatic effects.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ------------------------------------------------------ |
| `object` | `str` | | name of a single object or "all" |
| `state` | `int` | `-1` | object state or -1 for current state, 0 for all states |
| `cycles` | `int` | `10` | number of iterations \{default: 10} |
**See also:** `commands: sculpt_activate`, `sculpt_deactivate`, `settings: "sculpting" setting`, `all "sculpt_*" settings`
### cmd.sculpt\_purge
"sculpt\_purge" is an unsupported feature.
### cmd.select
"select" creates a named atom selection from a selection-expression.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `name` | | | |
| `selection` | | `''` | |
| `enable` | | `-1` | |
| `quiet` | | `1` | |
| `merge` | | `0` | |
| `state` | | `0` | |
| `domain` | | `''` | |
**See also:** `delete`
### cmd.select\_list
API only. Select by atom indices within a single object. Returns the number of selected atoms.
| Parameter | Type | Default | Description |
| --------- | ----------------- | ------- | ---------------------------------------------------- |
| `name` | `str` | | a unique name for the selection |
| `object` | `str` | | object name |
| `id_list` | | | |
| `state` | `int` | `0` | object state, to limit selection to atoms which have |
| `mode` | `id\|index\|rank` | `'id'` | \{default: id} |
| `quiet` | | `1` | |
### cmd.selection\_sc
| Parameter | Type | Default | Description |
| --------- | ---- | ----------------------------------- | ----------- |
| `sc` | | `` | |
| `gn` | | `` | |
### cmd.set
"set" changes global, object, object-state, or per-atom settings.
| Parameter | Type | Default | Description |
| ----------- | -------- | ------- | ------------------------------------ |
| `name` | `string` | | setting name |
| `value` | `string` | `1` | a setting value \{default: 1} |
| `selection` | `string` | `''` | name-pattern or selection-expression |
| `state` | | `0` | |
| `updates` | | `1` | |
| `log` | | `0` | |
| `quiet` | | `1` | |
**See also:** `get`, `set_bond`
### cmd.set\_atom\_property
Set an atom-level property
| Parameter | Type | Default | Description |
| ----------- | -------------------- | ------- | ---------------------------------------------------- |
| `name` | `string` | | Name of the property |
| `value` | `str/int/float/bool` | | Value to be set |
| `selection` | `string` | `'all'` | a selection-expression |
| `state` | `int` | `0` | Object state, 0 for all states, -1 for current state |
| `proptype` | `int` | `-1` | The type of the property, -1=auto, 1=bool, 2=int, |
| `quiet` | | `1` | |
**See also:** `set_property`, `iterate`, `alter`
### cmd.set\_bond
"set\_bond" changes per-bond settings for all bonds which exist between two selections of atoms.
| Parameter | Type | Default | Description |
| ------------ | -------- | ------- | --------------------------------------------- |
| `name` | `string` | | name of the setting |
| `value` | `string` | | new value to use |
| `selection1` | `string` | | first set of atoms |
| `selection2` | `string` | `None` | seconds set of atoms \{default: (selection1)} |
| `state` | | `0` | |
| `updates` | | `1` | |
| `log` | | `0` | |
| `quiet` | | `1` | |
### cmd.set\_color
"set\_color" defines a new color using the red, green, and blue (RGB) color components.
| Parameter | Type | Default | Description |
| --------- | -------- | ------- | ---------------------------------- |
| `name` | `string` | | name for the new or existing color |
| `rgb` | | | |
| `mode` | | `0` | |
| `quiet` | | `1` | |
**See also:** `recolor`
### cmd.set\_colorection
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `dict` | | | |
| `key` | | | |
### cmd.set\_colour
"set\_color" defines a new color using the red, green, and blue (RGB) color components.
| Parameter | Type | Default | Description |
| --------- | -------- | ------- | ---------------------------------- |
| `name` | `string` | | name for the new or existing color |
| `rgb` | | | |
| `mode` | | `0` | |
| `quiet` | | `1` | |
**See also:** `recolor`
### cmd.set\_dihedral
"set\_dihedral" changes the dihedral angle formed between the four bonded atoms provided. The atoms must be acyclic.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `atom1` | | | |
| `atom2` | | | |
| `atom3` | | | |
| `atom4` | | | |
| `angle` | | | |
| `state` | | `1` | |
| `quiet` | | `1` | |
### cmd.set\_discrete
Convert discrete to non-discrete object or vice versa.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `name` | | | |
| `discrete` | | `1` | |
| `quiet` | | `1` | |
### cmd.set\_frame
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `frame` | | `1` | |
| `mode` | | `0` | |
### cmd.set\_geometry
"set\_geometry" changes PyMOL's assumptions about the proper valence and geometry of atoms in the selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `selection` | | | |
| `geometry` | | | |
| `valence` | | | |
**See also:** `remove`, `attach`, `fuse`, `bond`, `unbond`
### cmd.set\_key
"set\_key" binds a specific python function to a key press. New in PyMOL 1.6.1: second argument can also be a string in PyMOL command syntax.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `key` | | | |
| `fn` | | `None` | |
| `arg` | | `()` | |
| `kw` | | `{}` | |
**See also:** `button`, `alias`
### cmd.set\_name
"set\_name" changes the name of an object or selection.
| Parameter | Type | Default | Description |
| ---------- | ---- | ------- | ----------- |
| `old_name` | | | |
| `new_name` | | | |
### cmd.set\_object\_color
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `color` | | | |
| `quiet` | | `1` | |
### cmd.set\_object\_ttt
"set\_object\_ttt" is an API-only function which sets the TTT matrix (view transformation) for an object. When a movie is defined and the object has key frames for object motions, then the key frames take priority and update the TTT matrix while the movie is playing. Unlike a homogenous matrix where the last row is always \[0,0,0,1], a TTT matrix may have a pre-translation vector in the last row.
| Parameter | Type | Default | Description |
| ------------ | ----- | ------- | ------------------------------------------- |
| `object` | `str` | | object name |
| `ttt` | | | |
| `state` | `int` | `0` | UNUSED, TTT matrices are not state specific |
| `quiet` | | `1` | |
| `homogenous` | `0/1` | `0` | NAME IS MISLEADING AND IMPLEMENTATION |
**See also:** `cmd.transform_object`, `cmd.matrix_reset`
### cmd.set\_property
Set an object-level property
| Parameter | Type | Default | Description |
| ---------- | -------------------- | ------- | ----------------------------------------------------- |
| `name` | `string` | | Name of the property |
| `value` | `str/int/float/bool` | | Value to be set |
| `object` | `string` | `'*'` | Space separated list of objects or \* for all objects |
| `state` | `int` | `0` | Object state, 0 for all states, -1 for current state |
| `proptype` | `int` | `-1` | The type of the property, -1=auto, 1=bool, 2=int, |
| `quiet` | | `1` | |
**See also:** `get_property`, `get_property_list`, `set_atom_property`
### cmd.set\_raw\_alignment
API only. Create an alignment object from lists of indices.
| Parameter | Type | Default | Description |
| --------- | ------ | ------- | -------------------------------------------------- |
| `name` | `str` | | alignment object name |
| `raw` | `list` | | list (columns) of lists with (model, index) tuples |
| `guide` | `str` | `''` | name of guide object |
| `state` | `int` | `1` | object state |
| `quiet` | | `1` | |
**See also:** `cmd.get_raw_alignment`
### cmd.set\_scene\_message
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | | |
| `message` | | | |
### cmd.set\_session
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `session` | | | |
| `partial` | | `0` | |
| `quiet` | | `1` | |
| `cache` | | `1` | |
| `steal` | | `-1` | |
### cmd.set\_state\_order
API only. Set the order of states for an object.
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | ----------- |
| `name` | `str` | | object name |
| `order` | | | |
| `quiet` | | `1` | |
### cmd.set\_symmetry
"set\_symmetry" defines or redefines the crystal and spacegroup parameters for a molecule or map object.
| Parameter | Type | Default | Description |
| ------------ | ----- | ------- | ------------------- |
| `selection` | `str` | | object name pattern |
| `a` | | | |
| `b` | | | |
| `c` | | | |
| `alpha` | | | |
| `beta` | | | |
| `gamma` | | | |
| `spacegroup` | | `'P1'` | |
| `state` | | `-1` | |
| `quiet` | | `1` | |
### cmd.set\_title
"set\_title" attaches a text string to the state of a particular object which can be displayed next to the object name when that state is active. This is useful for display the energies of a set of conformers.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | | |
| `state` | | | |
| `text` | | | |
### cmd.set\_view
"set\_view" sets viewing information for the current scene, including the rotation matrix, position, origin of rotation, clipping planes, and the orthoscopic flag.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `view` | | | |
| `animate` | | `0` | |
| `quiet` | | `1` | |
| `hand` | | `1` | |
**See also:** `get_view`
### cmd.set\_vis
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `dict` | | | |
### cmd.set\_wizard
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `wizard` | | `None` | |
| `replace` | | `0` | |
### cmd.set\_wizard\_stack
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `stack` | | `[]` | |
### cmd.show
"show" turns on representations for objects and selections.
| Parameter | Type | Default | Description |
| ---------------- | -------- | -------- | -------------------------------------- |
| `representation` | | `'wire'` | |
| `selection` | `string` | `''` | a selection-expression or name-pattern |
**See also:** `hide`, `enable`, `disable`
### cmd.show\_as
"as" turns on and off atom and bond representations.
| Parameter | Type | Default | Description |
| ---------------- | ---- | -------- | ----------- |
| `representation` | | `'wire'` | |
| `selection` | | `''` | |
**See also:** `show`, `hide`, `enable`, `disable`
### cmd.show\_help
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `cmmd` | | | |
### cmd.simple
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
### cmd.slice\_new
"slice\_map" creates a slice object from a map object.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `name` | | | |
| `map` | | | |
| `state` | | `1` | |
| `source_state` | | `0` | |
**See also:** `isomesh`, `isodot`, `load`
### cmd.smooth
"smooth" performs a window average of coordinate states.
| Parameter | Type | Default | Description |
| ----------- | ------- | ------- | ----------------------------------------------------- |
| `selection` | | `'all'` | |
| `passes` | | `1` | |
| `window` | | `5` | |
| `first` | | `1` | |
| `last` | | `0` | |
| `ends` | | `0` | |
| `quiet` | | `1` | |
| `cutoff` | `float` | `-1` | Distance cutoff for atom movement between two frames. |
| `pbc` | `0/1` | `1` | Consider periodic boundary conditions \{default: 1} |
**See also:** `load_traj`
### cmd.sort
"sort" reorders atoms in the structure. It usually only necessary to run this routine after an "alter" command which has modified the names of atom properties. Without an argument, sort will resort all atoms in all objects.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | `''` | |
**See also:** `alter`
### cmd.space
"space" selects a color palette (or color space).
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `space` | | `''` | |
| `gamma` | | `1.0` | |
| `quiet` | | `0` | |
**See also:** `color`
### cmd.spawn
"spawn" launches a Python script in a new thread which will run concurrently with the PyMOL interpreter. It can be run in its own namespace (like a Python module, default), a local name space, or in the global namespace.
| Parameter | Type | Default | Description |
| ----------- | ---- | ---------- | ----------- |
| `filename` | | | |
| `namespace` | | `'module'` | |
**See also:** `run`
### cmd.spectrum
"spectrum" colors atoms with a spectrum of colors based on an atomic property.
| Parameter | Type | Default | Description |
| --------------- | --------- | ----------- | -------------------------------------------------------------- |
| `expression` | | `'count'` | |
| `palette` | `string` | `'rainbow'` | palette name or space separated list of colors |
| `selection` | `string` | `'(all)'` | atoms to color \{default: (all)} |
| `minimum` | `float` | `None` | \{default: None (automatic)} |
| `maximum` | `float` | `None` | \{default: None (automatic)} |
| `byres` | `integer` | `0` | controls whether coloring is applied per-residue \{default: 0} |
| `quiet` | | `1` | |
| `interpolation` | | `'rgb'` | |
### cmd.spheroid
"spheroid" averages trajectory frames together to create an ellipsoid-like approximation of the actual anisotropic motion exhibited by the atom over a series of trajectory frames.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | `''` | |
| `average` | | `0` | |
### cmd.splash
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `mode` | | `0` | |
### cmd.split\_chains
Create a single object for each chain in selection
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `prefix` | | `None` | |
| `group` | | `None` | |
| `quiet` | | `1` | |
**See also:** `split_states`
### cmd.split\_states
"split\_states" separates a multi-state molecular object into a set of single-state molecular objects.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `object` | | | |
| `first` | | `1` | |
| `last` | | `0` | |
| `prefix` | | `None` | |
**See also:** `join_states`
### cmd.stereo
"stereo" activates or deactives stereo mode.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `toggle` | | `'on'` | |
| `quiet` | | `1` | |
### cmd.super
"super" performs a residue-based pairwise alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject outliers.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------------ | ----------- |
| `mobile` | | | |
| `target` | | | |
| `cutoff` | | `2.0` | |
| `cycles` | | `5` | |
| `gap` | | `-1.5` | |
| `extend` | | `-0.7` | |
| `max_gap` | | `50` | |
| `object` | | `None` | |
| `matrix` | | `'BLOSUM62'` | |
| `mobile_state` | | `0` | |
| `target_state` | | `0` | |
| `quiet` | | `1` | |
| `max_skip` | | `0` | |
| `transform` | | `1` | |
| `reset` | | `0` | |
| `seq` | | `0.0` | |
| `radius` | | `12.0` | |
| `scale` | | `17.0` | |
| `base` | | `0.65` | |
| `coord` | | `0.0` | |
| `expect` | | `6.0` | |
| `window` | | `3` | |
| `ante` | | `-1.0` | |
**See also:** `align`, `pair_fit`, `fit`, `rms`, `rms_cur`, `intra_rms`, `intra_rms_cur`
### cmd.symexp
"symexp" creates all symmetry-related objects for the specified object that occur within a cutoff about an atom selection.
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `prefix` | | | |
| `object` | | | |
| `selection` | | | |
| `cutoff` | | | |
| `segi` | | `0` | |
| `quiet` | | `1` | |
**See also:** `load`
### cmd.symmetry\_copy
"symmetry\_copy" copies symmetry information from one object to another.
| Parameter | Type | Default | Description |
| -------------- | ----- | ------- | ------------------------ |
| `source_name` | `str` | | object name |
| `target_name` | `str` | | object name pattern |
| `source_state` | `int` | `1` | object state (maps only) |
| `target_state` | `int` | `1` | object state (maps only) |
| `quiet` | | `1` | |
### cmd.sync
"sync" is an API-only function which waits until all current commmands have been executed before returning. A timeout can be used to insure that this command eventually returns.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `timeout` | | `1.0` | |
| `poll` | | `0.05` | |
**See also:** `frame`
### cmd.technical
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
### cmd.test
"dump" is an unsupported internal command.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `group` | | `0` | |
| `index` | | `0` | |
### cmd.toggle
"toggle" toggles the visibility of a representation within a selection.
| Parameter | Type | Default | Description |
| ---------------- | -------- | --------- | -------------------------------------- |
| `representation` | `string` | `'lines'` | named representation \{default: lines} |
| `selection` | `string` | `'all'` | atom selection \{default: all} |
**See also:** `show`, `hide`
### cmd.torsion
"torsion" rotates the torsion on the bond currently picked for editing. The rotated fragment will correspond to the first atom specified when picking the bond (or the nearest atom, if picked using the mouse).
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `angle` | | | |
**See also:** `edit`, `unpick`, `remove_picked`, `cycle_valence`
### cmd.transform\_object
"transform\_object" in an API-only function which applies a transformation matrix to an object. If setting "matrix\_mode" > 0 and selection is empty, then this function operates on the TTT (movie) matrix.
| Parameter | Type | Default | Description |
| ------------ | ----- | ------- | -------------------------------------------------------- |
| `name` | `str` | | object name |
| `matrix` | | | |
| `state` | `int` | `-1` | object state \{default: -1} |
| `log` | `0/1` | `0` | write action to log file (only applies if object is a |
| `selection` | `str` | `''` | atom selection (only applies to molecular objects, |
| `homogenous` | `0/1` | `0` | if 0, then matrix\[12:15] may contain a pre-translation, |
| `transpose` | `0/1` | `0` | matrix is 0=row-major, 1=column-major \{default: 0} |
**See also:** `cmd.transform_selection`, `cmd.set_object_ttt`, `cmd.matrix_reset`
### cmd.transform\_selection
"transform\_selection" transforms the atomic coordinates of a selection.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `selection` | | | |
| `matrix` | | | |
| `state` | | `-1` | |
| `log` | | `0` | |
| `homogenous` | | `0` | |
| `transpose` | | `0` | |
### cmd.translate
"translate" translates the atomic coordinates of atoms in a selection. Alternatively, is modifies the matrix associated with a particular object or object-state.
| Parameter | Type | Default | Description |
| ------------- | -------- | ----------------- | ------------------------------------------------------------- |
| `vector` | | `[0.0, 0.0, 0.0]` | |
| `selection` | `string` | `'all'` | atoms whose coordinates should be modified \{default: all} |
| `state` | `0` | `-1` | all states are modified |
| `camera` | | `1` | |
| `object` | `string` | `None` | object name (only if rotating object matrix) \{default: None} |
| `object_mode` | | `0` | |
### cmd.translate\_atom
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `sele1` | | | |
| `v0` | | | |
| `v1` | | | |
| `v2` | | | |
| `state` | | `0` | |
| `mode` | | `0` | |
| `log` | | `0` | |
### cmd.turn
"turn" rotates the camera about one of the three primary axes, centered at the origin.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `axis` | | | |
| `angle` | | | |
**See also:** `move`, `rotate`, `translate`, `zoom`, `center`, `clip`
### cmd.unblock\_flush
### cmd.unbond
"unbond" removes all bonds between two selections.
| Parameter | Type | Default | Description |
| --------- | ---- | --------- | ----------- |
| `atom1` | | `'(pk1)'` | |
| `atom2` | | `'(pk2)'` | |
| `quiet` | | `1` | |
**See also:** `bond`, `fuse`, `remove_picked`, `attach`, `detach`, `replace`
### cmd.undo
"undo" restores the previous conformation of the object currently being edited.
**See also:** `redo`, `push_undo`
### cmd.ungroup
"ungroup" removes an object from a group object, returning it to the top level.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `members` | | | |
| `quiet` | | `1` | |
**See also:** `group`
### cmd.uniquify
Make `identifier` unique with respect to reference selection.
| Parameter | Type | Default | Description |
| ------------ | ----- | ------- | -------------------------------------------- |
| `identifier` | `str` | | atom identifier (chain, segi, etc.) |
| `selection` | `str` | | atom selection to modify |
| `reference` | `str` | `''` | atom selection whose identifiers must not be |
| `quiet` | | `1` | |
### cmd.unlock
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `result` | | `None` | |
### cmd.unmask
"unmask" reverses the effect of "mask" on the indicated atoms.
| Parameter | Type | Default | Description |
| ----------- | ---- | --------- | ----------- |
| `selection` | | `'(all)'` | |
| `quiet` | | `1` | |
**See also:** `mask`, `protect`, `deprotect`, `mouse`
### cmd.unpick
"unpick" deletes the special "pk" atom selections (pk1, pk2, etc.) used in atom picking and molecular editing.
**See also:** `edit`
### cmd.unset
"unset" clears a setting and restores its default value. WARNING: The behavior for global settings changed in PyMOL 2.5. Previously, "unset settingname" would set the global value of "settingname" to zero/off instead of the default value. To set a setting to zero, do "set settingname, 0".
| Parameter | Type | Default | Description |
| ----------- | ---- | ------- | ----------- |
| `name` | | | |
| `selection` | | `''` | |
| `state` | | `0` | |
| `updates` | | `1` | |
| `log` | | `0` | |
| `quiet` | | `1` | |
**See also:** `unset_deep`, `set`, `set_bond`
### cmd.unset\_bond
"unset\_bond" removes a per-bond setting for a given set of bonds.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `name` | | | |
| `selection1` | | | |
| `selection2` | | `None` | |
| `state` | | `0` | |
| `updates` | | `1` | |
| `log` | | `0` | |
| `quiet` | | `1` | |
### cmd.unset\_deep
Unset all object, object-state, atom, and bond level settings. Note: Does currently NOT unset atom-state level settings. Check for atom-state level settings with: PyMOL> iterate\_state 1, \*, print(list(s)) Unset e.g. atom-state level "label\_screen\_point" (index 728) with: PyMOL> alter\_state 1, \*, del s\[728]
| Parameter | Type | Default | Description |
| ---------- | ----- | ------- | ------------------------------------------------------- |
| `settings` | `str` | `''` | space separated list of setting names or empty string |
| `object` | `str` | `'*'` | name of one object or \* for all objects \{default: \*} |
| `updates` | | `1` | |
| `quiet` | | `1` | |
### cmd.update
"update" transfers coordinates from one selection to another.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `target` | | | |
| `source` | | | |
| `target_state` | | `0` | |
| `source_state` | | `0` | |
| `matchmaker` | | `1` | |
| `quiet` | | `1` | |
**See also:** `load`
### cmd.usalign
"usalign" performs a TM-align structural superposition of two protein structures. Unlike "align" and "super", it uses TM-score optimization, which is length-independent and more suitable for comparing proteins with different lengths or low sequence identity. Only CA of proteins and C4' of nucleic acids are considered for alignment.
| Parameter | Type | Default | Description |
| -------------- | ------------- | ------- | --------------------------------------------------- |
| `mobile` | `str` | | atom selection of mobile object |
| `target` | `str` | | atom selection of target object |
| `mobile_state` | `int` | `1` | object state of mobile selection \{default: 1} |
| `target_state` | `int` | `1` | object state of target selection \{default: 1} |
| `quiet` | `int` | `1` | |
| `transform` | `int` | `1` | apply superposition transform \{default: 1} |
| `object` | `str \| None` | `None` | name of alignment object to create \{default: None} |
| `fast` | `int` | `0` | use fast mode with fewer iterations \{default: 0} |
**See also:** `align`, `super`, `cealign`, `pair_fit`, `fit`
### cmd.valence
"valence" modifies the valences of all existing bonds formed between two atom selections.
| Parameter | Type | Default | Description |
| -------------- | ---- | ------- | ----------- |
| `order` | | | |
| `selection1` | | `None` | |
| `selection2` | | `None` | |
| `source` | | `''` | |
| `target_state` | | `0` | |
| `source_state` | | `0` | |
| `reset` | | `1` | |
| `quiet` | | `1` | |
| `symop` | | `''` | |
**See also:** `unbond`, `fuse`, `attach`, `replace`, `remove_picked`
### cmd.vdw\_fit
"vdw\_fit" is an unsupported feature.
| Parameter | Type | Default | Description |
| ------------ | ---- | ------- | ----------- |
| `selection1` | | | |
| `selection2` | | | |
| `state1` | | `1` | |
| `state2` | | `1` | |
| `buffer` | | `0.24` | |
| `quiet` | | `1` | |
### cmd.view
"view" saves and restore camera views.
| Parameter | Type | Default | Description |
| --------- | ---- | ---------- | ----------- |
| `key` | | | |
| `action` | | `'recall'` | |
| `animate` | | `-1` | |
**See also:** `scene`, `set_view`, `get_view`
### cmd.viewport
"viewport" changes the size of the graphics display area.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `width` | | `-1` | |
| `height` | | `-1` | |
### cmd.volume
"volume" creates a volume object from a map object.
| Parameter | Type | Default | Description |
| -------------- | ----- | ------- | ----------------------------- |
| `name` | | | |
| `map` | | | |
| `ramp` | `str` | `''` | named color ramp \{default: } |
| `selection` | | `''` | |
| `buffer` | | `0.0` | |
| `state` | | `1` | |
| `carve` | | `None` | |
| `source_state` | | `0` | |
| `quiet` | | `1` | |
**See also:** `map_new`, `isosurface`, `isomesh`, `volume_color`, `volume_ramp_new`
### cmd.volume\_color
Set or get the volume colors.
| Parameter | Type | Default | Description |
| ------------ | ----- | ------- | ------------------------ |
| `name` | `str` | | volume object name |
| `ramp` | | `''` | |
| `state` | `int` | `-1` | state of volume to color |
| `quiet` | | `1` | |
| `_guiupdate` | | `True` | |
### cmd.volume\_panel
Open an interactive volume ramp panel
| Parameter | Type | Default | Description |
| --------- | ----- | ------- | --------------------- |
| `name` | `str` | | name of volume object |
| `quiet` | | `1` | |
| `_noqt` | | `0` | |
### cmd.volume\_ramp\_new
Register a named volume ramp which can be used as a preset when creating or coloring volumes. The name will appear in the internal menu at "A > volume" and "C".
| Parameter | Type | Default | Description |
| --------- | -------- | ------- | ------------------------------------------- |
| `name` | `string` | | name of the new ramp |
| `ramp` | `list` | | space delimited list of value, color, alpha |
**See also:** `volume`, `volume_color`
### cmd.window
"window" controls the visibility of PyMOL's output window
| Parameter | Type | Default | Description |
| --------- | ---- | -------- | ----------- |
| `action` | | `'show'` | |
| `x` | | `0` | |
| `y` | | `0` | |
| `width` | | `0` | |
| `height` | | `0` | |
### cmd.wizard
"wizard" launches on of the built-in wizards. There are special Python scripts which work with PyMOL in order to obtain direct user interaction and easily peform complicated tasks.
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `name` | | `None` | |
### cmd.write\_html\_ref
| Parameter | Type | Default | Description |
| --------- | ---- | ------- | ----------- |
| `file` | | | |
### cmd.zoom
"zoom" scales and translates the window and the origin to cover the atom selection.
| Parameter | Type | Default | Description |
| ----------- | -------- | ------- | ---------------------------------------------------- |
| `selection` | `string` | `'all'` | selection-expression or name pattern \{default: all} |
| `buffer` | `float` | `0.0` | distance \{default: 0} |
| `state` | `0` | `0` | uses all coordinate states \{default} |
| `complete` | | `0` | |
| `animate` | `0` | `0` | no animation |
**See also:** `origin`, `orient`, `center`