Commands - tenmol

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`		`<class 'pymol.shortcut.Shortcut'>`
`gnot`		`<opaque>`

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`		`<class 'pymol.shortcut.Shortcut'>`
`gnot`		`<opaque>`

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/

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`		`<class 'pymol.shortcut.Shortcut'>`
`gnot`		`<opaque>`

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: <sele1>}
`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`		`<class 'pymol.shortcut.Shortcut'>`
`gn`		`<opaque>`

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 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`		`<class 'pymol.shortcut.Shortcut'>`
`gn`		`<opaque>`

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

​cmd.LockCM

​cmd.SafeEvalNS

​cmd.Shortcut

​cmd.abort

​cmd.accept

​cmd.add_bond

​cmd.align

​cmd.alignto

​cmd.alphatoall

​cmd.alter

​cmd.alter_list

​cmd.alter_state

​cmd.angle

​cmd.api

​cmd.as_pathstr

​cmd.assign_stereo

​cmd.async_

​cmd.attach

​cmd.auto_measure

​cmd.backward

​cmd.bg_color

​cmd.bg_colour

​cmd.block_flush

​cmd.bond

​cmd.button

​cmd.cache

​cmd.callout

​cmd.capture

​cmd.cartoon

​cmd.cd

​cmd.cealign

​cmd.center

​cmd.centerofmass

​cmd.check

​cmd.clean

​cmd.clip

​cmd.cls

​cmd.color

​cmd.color_deep

​cmd.colour

​cmd.commands

​cmd.config_mouse

​cmd.contour_sc

​cmd.copy

​cmd.copy_image

​cmd.copy_to

​cmd.count_atoms

​cmd.count_discrete

​cmd.count_frames

​cmd.count_states

​cmd.create

​cmd.curve_new

​cmd.cycle_valence

​cmd.decline

​cmd.del_colorection

​cmd.delete

​cmd.delete_states

​cmd.deprotect

​cmd.desaturate

​cmd.deselect

​cmd.dihedral

​cmd.dirty

​cmd.dirty_wizard

​cmd.disable

​cmd.dist

​cmd.distance

​cmd.download_chem_comp

​cmd.drag

​cmd.draw

​cmd.dss

​cmd.dump

​cmd.edit

​cmd.edit_mode

​cmd.editing_ring

​cmd.enable

​cmd.ending

​cmd.exp_path

​cmd.extendaa

​cmd.extra_fit

​cmd.extract

cmd.LockCM

cmd.SafeEvalNS

cmd.Shortcut

cmd.abort

cmd.accept

cmd.add_bond

cmd.align

cmd.alignto

cmd.alphatoall

cmd.alter

cmd.alter_list

cmd.alter_state

cmd.angle

cmd.api

cmd.as_pathstr

cmd.assign_stereo

cmd.async_

cmd.attach

cmd.auto_measure

cmd.backward

cmd.bg_color

cmd.bg_colour

cmd.block_flush

cmd.bond

cmd.button

cmd.cache

cmd.callout

cmd.capture

cmd.cartoon

cmd.cd

cmd.cealign

cmd.center

cmd.centerofmass

cmd.check

cmd.clean

cmd.clip

cmd.cls

cmd.color

cmd.color_deep

cmd.colour

cmd.commands

cmd.config_mouse

cmd.contour_sc

cmd.copy

cmd.copy_image

cmd.copy_to

cmd.count_atoms

cmd.count_discrete

cmd.count_frames

cmd.count_states

cmd.create

cmd.curve_new

cmd.cycle_valence

cmd.decline

cmd.del_colorection

cmd.delete

cmd.delete_states

cmd.deprotect

cmd.desaturate

cmd.deselect

cmd.dihedral

cmd.dirty

cmd.dirty_wizard

cmd.disable

cmd.dist

cmd.distance

cmd.download_chem_comp

cmd.drag

cmd.draw

cmd.dss

cmd.dump

cmd.edit

cmd.edit_mode

cmd.editing_ring

cmd.enable

cmd.ending

cmd.exp_path

cmd.extendaa

cmd.extra_fit

cmd.extract