Functions for User Commands

The chimera.core.commands module contains Python functions for the core commands available from the Chimera command-line. Tools define additional commands noted with a (*) and their code location is described with the function descriptions.

buriedarea - Compute buried area between atomic structures
camera - Change camera settings
close - Close models
color - Color atoms, ribbons and surfaces
colordef - Define new colors
command_line * - Hide or show the command line
contacts * - Make a buried area contact graph
crossfade - Fade between scenes for movie making
crosslinks - Move atomic structures to minimize crosslinks
delete - Delete models
display - Display atoms
echo - Write message to log
exit - Quit
export - Export files
fitmap - fit atomic structures in density maps
help - Show documentation
ks - Enable keyboard shortcuts
lighting - Change lighting parameters
list - List open models
log * - Hide and show the log
material - Change surface material light reflection properties
molmap - Calculate a density map from atoms
mousemodes * - Hide or show mouse modes panel
movie * - Record videos
move - Move camera
oculus - Enable Oculus Rift headset
open - Open data files
pdbimages - Render PDB assembly images
perframe - Run a command for every rendered frame
pwd - Present working directory
rcolor - Color ribbons
roll - Rotate models
ribbon - Display atomic structure ribbons
run - Run a user command string
sasa - Compute solvent accessible surface area
save - Save sessions, images, density maps...
scolor - Color surfaces
set - Set rendering effects (background color, silhouettes)
snav - Enable space navigator input device
split - Split atomic structures into pieces
stop - Stop motion
style - Change atom display style
surface - Compute a molecular surface
sym - Show molecular assemblies involving symmetry
title * - Show text titles with graphics
toolshed * - Control the Tool Shed user interface
turn - Rotate models
view - Move camera to view all models
volume - Change density map display settings
vop - Filter density maps
vseries - Play density map time series
wait - Wait before executing next command

buriedarea

buriedarea(session, atoms1, with_atoms2=None, probe_radius=1.4)

Compute buried solvent accessible surface (SAS) area between two sets of atoms. This is the sum of the SAS area of each set of atoms minus the SAS area of the combined sets of atoms, that difference divided by two since each set of atoms has surface at the interface, so the interface area is defined as half the buried area. Atoms not specified in either atom set are ignored when considering where the probe sphere can reach.

Parameters:

atoms1 : Atoms

First set of atoms.

with_atoms2 : Atoms

Second set of atoms – must be disjoint from first set.

probe_radius : float

Radius of the probe sphere.

camera

camera(session, mode=None, field_of_view=None, eye_separation=None, screen_width=None, depth_scale=None)

Change camera parameters.

Parameters:

mode : N/A

Currently not used.

field_of_view : float

Horizontal field of view in degrees.

eye_separation : float

Distance between eyes for stereo camera modes. Can use any units and must specify screen width too. Only eye_separation divided by screen width is used.

screen_width : float

Width of screen in same units as eye separation. Only used for stereo camera modes.

depth_scale : float

Scale the eye separation by this factor. Only used in stereo camera modes.

close

close(session, model_ids=None)

Close models.

Parameters:

model_ids : list of model ids

These models and any submodels are closed. If no model ids are specified then all models are closed.

color

color(session, spec, color=None, target=None, sequential=None, cmap=None, cmap_range=None)

Color atoms, ribbons, surfaces, ....

Parameters:

spec : specifier

Which objects to color.

color : Color

Color can be a standard color name or “byelement”, “byhetero” or “bychain” .

target : string

Characters indicating what to color, a = atoms, c = cartoon, s = surfaces, m = models, n = non-molecule models, l = labels, r = residue labels, b = bonds, p = pseudobonds, d = distances. Everything is colored if no target is specified.

sequential : string

Value can only be “chains”, assigns each chain a color from a color map.

cmap : Colormap

Color map to use with sequential coloring

cmap_range : 2 comma-separated floats or “full”

Specifies the range of value used for sampling from a color map.

colordef

colordef(session, name, color=None)

Create a user defined color.

uncolordef(session, name)

Remove a user defined color.

command_line

Functions defined in chimera.cmd_line.cmd

command_line_hide(session)

Hide the command line.

command_line_show(session)

Show the command line.

contacts

Function found in chimera.contacts.cmd

contacts(session, atoms=None, probe_radius=1.4)

Compute buried solvent accessible surface areas between chains and show a 2-dimensional network graph depicting the contacts.

Parameters:

atoms : Atoms

probe_radius : float

crossfade

crossfade(session, frames=30)

Fade from the current view to the next drawn view. Used in movie recording.

Parameters:

frames : integer

Linear interpolate between the current and next image over this number of frames.

delete

delete(session, atoms)

Delete atoms.

Parameters:

atoms : Atoms collection

Delete these atoms. If all atoms of a model are closed then the model is closed.

display

display(session, spec=None)

Display specified atoms.

Parameters:

spec : atom specifier

Show the specified atoms. If no atom specifier is given then all atoms are shown. Atoms that are already shown remain shown.

undisplay(session, spec=None)

Hide specified atoms.

Parameters:

spec : atom specifier

Hide the specified atoms. If no atom specifier is given then all atoms are hidden.

echo

echo(session, text='')

Echo text to the log.

Parameters:

text : string

The text to log.

exit

exit(session)

Quit the program.

export

export(session, filename, **kw)

fitmap

fitmap(session, atoms_or_map, in_map=None, subtract_maps=None, metric=None, envelope=True, resolution=None, shift=True, rotate=True, symmetric=False, move_whole_molecules=True, search=0, placement='sr', radius=None, cluster_angle=6, cluster_shift=3, asymmetric_unit=True, level_inside=0.1, sequence=0, max_steps=2000, grid_step_min=0.01, grid_step_max=0.5, list_fits=None, each_model=False)

Fit an atomic model or a map in a map using a rigid rotation and translation by locally optimizing correlation. There are four modes: 1) fit all models into map as a single rigid group, 2) fit each model into the map separately, 3) fit each model separately while subtracting others (sequence mode), or 4) use random starting positions when fitting (search mode).

Parameters:

atoms_or_map

Atoms or map that will be moved.

in_map : Volume

Target density map to fit into.

subtract_maps : Atoms

Subtract map for these atoms from the target map before fitting.

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Mode

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each_model : bool

Whether to fit each model independently or all as one rigid group.

sequence : integer

Fit each model in sequence subtracting other models first for this number of specified fits.

search : integer

Fit using N randomized initial placements and cluster similar results.

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Fitting settings

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metric : ‘overlap’, ‘correlation’, or ‘cam’

Optimization function to use. Overlap is pointwise sum. Cam is correlation about mean (ie. mean value is subtracted from maps before computing correlation).

envelope : bool

Whether to consider fit only within lowest displayed contour level if moving map.

resolution : float

Resolution for making simulated maps from atomic models. Required when correlation or cam metric is used and atomic models are being fit.

shift : bool

Allow translation when fitting.

rotate : bool

Allow rotation when fitting.

symmetric : bool

Whether to use symmetry of the target map to take account of clashes between copies of the fit models.

max_steps: integer

Maximum number of gradient ascent steps to take

grid_step_max : float

Maximum motion during a fitting step in grid index units.

grid_step_min : float

The fit is considered converged when Motion less than this value (grid index units).

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Search options

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placement : ‘sr’, ‘s’, or ‘r’

Whether random placements should include shift and rotation

radius : float

Limits the random placements to within this distance of the starting position.

cluster_angle : float

Rotational difference for a fit to form a new cluster.

cluster_shift : float

Shift difference for a fit to form a new cluster.

asymmetric_unit : bool

List only one symmetrically equivalent fit position if the target map has symmetry.

level_inside : float

Fraction of fit atoms or map that must be inside the target map contour level in order to keep the fit.

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Output options

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move_whole_molecules : bool

Move entire molecules, or only the atoms that were specified.

list_fits : bool

Show the fits in a dialog.

help

help(session, command_name=None)

Display help.

Parameters:

command_name : string

Show documentation for the specified command. If no command is specified then the names of all commands are shown. If the command name “all” is given then a synopsis for each command is shown. The command name can be abbreviated.

ks

ks(session, shortcut=None)

Enable keyboard shortcuts. Keys typed in the graphics window will be interpreted as shortcuts.

Parameters:

shortcut : string

Keyboard shortcut to execute. If no shortcut is specified switch to shortcut input mode.

lighting

lighting(session, preset=None, direction=None, intensity=None, color=None, fill_direction=None, fill_intensity=None, fill_color=None, ambient_intensity=None, ambient_color=None, fixed=None, shadows=None, quality_of_shadows=None, depth_bias=None, multi_shadow=None, ms_map_size=None, ms_depth_bias=None)

Set lighting parameters. There are 2 directional lights, a key light and a fill light, in addition to ambient lighting. The key light can cast a shadow, and shadows cast from multiple uniformly distributed directions can produce ambient shadowing (aka “ambient occlusion”). Parameters that are not specified retain their current value. If no options are specified then the current settings are printed to the log.

Parameters:

preset : string

Names a standard set of lighting parameters. Allowed values are “default”, “simple”, “full”, “soft” and “flat”. Simple is the same as default and has no shadows. Full includes direct and ambient shadows. Soft includes ambient shadows from 64 directions and no direct lighting. Flat has only anbient lighting and no shadows with silhouettes enabled. Specifying a preset only specifies some of the lighting parameters. Specifying other options overrides the preset values.

direction : 3 floats

Key light direction as vector. Does not have to have unit length – it will be normalized. Points in the direction the light shines. The viewing direction is along -z. Initially is pointing down to the right (1,-1,-1).

intensity : float

Key light intensity. This is a brightness scale factor. Initial value 1.

color : Color

Key light color, initial value RGB = (1,1,1).

fill_direction : 3 floats

Fill light direction. Initially is pointing from lower left (-0.2,-0.2,-0.959).

fill_intensity : float

Fill light intensity. Initial value 0.5.

fill_color : Color

Fill light color, initial value RGB = (1,1,1).

ambient_intensity : float

Ambient light intensity. Initial value 0.4.

ambient_color : Color

Ambient color, initial value RGB = (1,1,1).

fixed : bool

Whether light directions are fixed in scene coordinates or move with the camera. Initial value fixed = false.

shadows : bool

Whether to show shadows. Initial value false.

quality_of_shadows : string or int

Shadows are rendered with a 2 dimensional texture. Pixelated shadow edges result from using small texture sizes. Value can be “coarse” (1024), “normal” (2048), “fine” (4096), “finer” (8192), or an integer value can be specified.

depth_bias : float

To avoid a surface shadowing itself due to numerical rounding errors an bias distance is used. This is a fraction of the scene diameter. Initial value 0.005.

multi_shadow : int

How many directions to use for casting ambient shadows. Value 0 means no ambient shadows. The soft preset uses 64 directions. Initial value 0.

ms_map_size : int

Size of one 2-dimensional texture holding all the ambient shadow maps. Small values give coarser shadows that give a smoother appearance when many shadows ar rendered. Initial value 128.

ms_depth_bias : float

Depth bias to avoid surface self shadowing for ambient shadows as a fraction of the scene diameter. Because small shadow map sizes are typically used a larger bias is needed than for directional shadows. Initial value 0.05.

list

list(session)

List the open model ids and names.

log

Function found in chimera.log.cmd

log(session, show=None, hide=None, warning_dialog=None, error_dialog=None, test=None)

Control setting for the Log window.

Parameters:

show : bool

hide : bool

warning_dialog : bool

If true, warnings popup a separate dialog, if false no warning dialog is shown. In either case the warning appears in the log text.

error_dialog : bool

If true, errors popup a separate dialog, if false no error dialog is shown. In either case the errors appears in the log text.

test : bool

Test logging of various types of messages.

material

material(session, preset=None, reflectivity=None, specular_reflectivity=None, exponent=None, ambient_reflectivity=None)

Change surface material properties controlling the reflection of light. Currently all models use the same material properties.

Parameters:

preset : string

Can be “default”, “shiny” or “dull”. Default sets all material properties to there default values. Shiny sets specular reflectivity to 1. Dull sets specular reflectivity to 0.

reflectivity : float

Fraction of directional light reflected diffusely (reflected equally in all directions). Initial value 0.8.

specular_reflectivity : float

Fraction of key light reflected specularly (mirror reflection with some spread given by exponent. Initial value 0.8.

exponent : float

Controls specularly reflected light scaling intensity by a factor of cosine(x) raised to the exponent power, where x is the between the mirror reflection direction and the view direction. Larger values produce smaller specular highlight spots on surfaces. Initial value 30.

ambient_reflectivity : float

Fraction of ambient light reflected. Initial value 0.8.

molmap

molmap(session, atoms, resolution, gridSpacing=None, edgePadding=None, cutoffRange=5, sigmaFactor=0.22507907903927651, balls=False, symmetry=None, center=(0, 0, 0), axis=(0, 0, 1), coordinateSystem=None, displayThreshold=0.95, modelId=None, replace=True, showDialog=True)

Create a density map by placing Gaussians centered on atoms.

Parameters:

atoms : Atoms

resolution : float

grid_spacing : float

Default is 1/3 resolution.

edge_padding : float

Default is 3 times resolution.

cutoff_range : float

In standard deviations.

sigma_factor : float

Scale factor equal to standard deviation / resolution, default 1/(pi*sqrt(2)).

balls : bool

Use balls instead of Gaussians

symmetry : not supported

Apply symmetry operations to atoms

center : 3 floats or atom spec

Center of symmetry.

axis : 3 floats

Axis of symmetry.

coordinate_system : model spec

Coordinate system of symmetry.

display_threshold : float

Initial contour level as fraction of total density, default 0.95.

model_id : list of integers

replace : bool

Default true

show_dialog : bool, not supported

mousemodes

Functions defined in chimera.mouse_modes.cmd

mousemodes_hide(session)

Hide the mouse modes icon panel.

mousemodes_show(session)

Show the mouse modes icon panel.

move

move(session, axis, distance, frames=None)

Shift the scene. Actually the camera is shifted and the models stay fixed.

Parameters:

axis : 3 comma-separated numbers

Defines the axis in scene coordinates to shift along.

distance : float

Distance to shift in scene units.

frames : integer

Repeat the shift for N frames.

movie

Functions defined in chimera.movie.moviecmd

movie_record(session, directory=None, pattern=None, format=None, size=None, supersample=1, limit=15000)

Start recording a movie.

Parameters:

directory : string

A temporary directory for saving image files before the movie is encoded. By default a temporary system directory is created.

pattern : string

File name including a printf style specification like “%04d” for the frame number for saving images.

format : string

Image file format (default ppm) for saving frames.

size : 2 int

Width and height in pixels of movie.

supersample : int

Amount of supersampling when saving individual image frames.

limit : int

Maximum number of frames to save. This is a safe guard so that the entire computer disk storage is not filled with images if a movie recording is never stopped.

movie_encode(session, output=None, format=None, quality=None, qscale=None, bitrate=None, framerate=25, round_trip=False, reset_mode='clear', wait=False)

Enode images captured with movie record command creating a movie file. This uses the standalone video encoding program ffmpeg which is included with Chimera.

Parameters:

output : list of strings

Filenames of movie output files. By specifying multiple files, different video encoding formats can be made.

format : string

Format of video file to write. If not specified, the file suffix determines the format.

quality : string

Quality of video, higher quality results in larger file size. Qualities are “highest”, “higher”, “high”, “good”, “medium”, “fair”, “low”. Default “good”. This overrides the qscale and bitrate options.

qscale : int

Quality scale parameter used by some video codecs. This overrides the bitrate option.

bitrate : int

Target bit rate for video encoding in Kbits/second.

framerate : int

Frames per second that video should playback at in a video player.

round_trip : bool

If true, the images are played forward and than backward so movie ends where it began. This is used for making movies that loop without a jump between the last frame and first frame.

reset_mode : string

Whether to keep or delete the image files that were captured after the video files is made. Values are “clear”, “keep” or “none”. Default “clear” means the image files are deleted.

wait : bool

Whether to wait until movie encoding is finished before the command returns. Default false means the command can return before the video encoding is complete.

movie_crossfade(session, frames=25)

Linear interpolate between the current graphics image and the next image over a specified number of frames.

movie_duplicate(session, frames=25)

Repeat the current image frame a specified number of frames so that the video does not change during playback.

movie_stop(session)

Stop recording video frames. Using the movie encode command also stops recording.

movie_abort(session)

Stop movie recording and delete any recorded frames.

movie_reset(session, reset_mode='clear')

Clear images saved with movie record.

movie_ignore(session, ignore=True)

Ignore subsequent movie commands except for the movie ignore command. This can be used to run a movie recording script without recording the movie.

movie_status(session)

Report recording status such as number of frames saved to the log.

movie_formats(session)

Report the available video formats to the log.

oculus

oculus(session, enable, pan_speed=None)

Enable stereo viewing and head motion tracking with an Oculus Rift headset.

Parameters:

enable : bool

Enable or disable use of an Oculus Rift headset. The device must be connected and powered on to enable it. A new full screen window will be created on the Oculus device. Graphics will not be updated in the main Chimera window because the different rendering rates of the Oculus and a conventional display will cause stuttering of the Oculus graphics. Also the Side View panel in the main Chimera window should be closed to avoid stuttering.

pan_speed : float

Controls how far the camera moves in response to tranlation head motion. Default 5.

open

open(session, filename, id=None, as_=None)

Open a file.

Parameters:

filename : string

A path to a file (relative to the current directory), or a database id code to fetch prefixed by the database name, for example, pdb:1a0m, mmcif:1jj2, emdb:1080. A 4-letter id that is not a local file is interpreted as an mmCIF fetch.

id : tuple of integer

The model id number to use for this data set.

as_ : Not sure what this is

pdbimages

pdbimages(session, directory='.', subdirectories=True, width=400, height=400, supersample=2, image_suffix='.png', exclude=['1m4x.cif'], log_file=None)

Assembly images command for batch rendering mmCIF assembly images. This is for the Protein DataBank to render images.

Parameters:

directory : string

Find all files with suffix .cif in this directory and recursively in subdirectories.

subdirectories : bool

Whether to recursively search subdirectories for .cif files.

width : integer

Width in pixels of saved image.

height : integer

Height in pixels of saved image.

supersample : integer

Supersampling makes image N-fold larger than averages down to smooth object images.

image_suffix : string

File suffix for images, used to determine image format (e.g. .png, .jpg, .tif)

exclude : list of strings

File names to exclude from rendering (some large files cause graphics crashes).

log_file : string

Path to file to write log messages as each mmCIF file is rendered.

perframe

perframe(session, command, frames=None, interval=1, format=None, zero_pad_width=None, range=None, show_commands=False)

Execute specified command each frame, typically used during movie recording.

Parameters:

command : string

The command to be run each frame, optionally containing “$1” which will be replaced by the frame number starting at 0.

frames : int

Number of frames to execute the specified command.

interval : int

Run the command only every Kth frame.

format : string

Printf style format (e.g. %d, %.3f) for substituting value in for $1.

zero_pad_width : int

Field width in characters used when substituting $1 left padded with zeros.

range : 2 or 3 int

start,end[,step] integer or float range of values to substitute for $1 instead of frame number.

show_commands : bool

Whether to echo commands to log.

pwd

pwd(session)

Report the current directory to the log.

rcolor

rcolor(session, color, spec=None)

Color ribbons.

Parameters:

color : Color

spec : atom specifier

Set ribbon color for these residues.

roll

roll(session, axis=(0, 1, 0), angle=1.5, frames=-1)

Rotate the scene. Same as the turn command with infinite frames argument.

Parameters:

axis : 3 comma-separated numbers

Defines the axis in scene coordinates to rotate about.

angle : float

Rotation angle in degrees.

frames : integer

Repeat the rotation for N frames.

ribbon

ribbon(session, spec=None)

Display ribbons for specified residues.

Parameters:

spec : atom specifier

Show ribbons for the specified residues. If no atom specifier is given then ribbons are shown for all residues. Residues that are already shown as ribbons remain shown as ribbons.

unribbon(session, spec=None)

Undisplay ribbons for specified residues.

Parameters:

spec : atom specifier

Hide ribbons for the specified residues. If no atom specifier is given then all ribbons are hidden.

run

run(session, text, downgrade_errors=False)

execute a textual command

Parameters:

text : string

The text of the command to execute.

downgrade_errors : bool

True if errors in the command should be logged as informational.

sasa

sasa(session, atoms=None, probe_radius=1.4)

Compute solvent accessible surface area.

Parameters:

atoms : Atoms

A probe sphere is rolled over these atoms ignoring collisions with any other atoms.

probe_radius : float

Radius of the probe sphere.

save

save(session, filename, width=None, height=None, supersample=None, format=None)

Save data, sessions, images.

Parameters:

filename : string

File to save. File suffix determines what type of file is saved unless the format option is given. For sessions the suffix is .c2ses. Image files can be saved with .png, .jpg, .tif, .ppm, .gif suffixes.

width : integer

Width of image in pixels for saving image files. If width is not specified the current graphics window width is used.

height : integer

Height of image in pixels for saving image files.

supersample : integer

Supersampling for saving images. Makes an image N times larger in each dimension then averages to requested image size to produce smoother object edges. Values of 2 or 3 are most useful, with little improvement for larger values.

format : string

File format for saving images. If not specified then the filename suffix is used to identify the format.

scolor

scolor(session, atoms=None, color=None, byatom=False, esp=None)

Color surfaces using a variety of methods, for example, to match nearby atom colors, or use a single color, or color by electrostatic potential, or color radially. TODO: Only a few options are currently supported.

set

set(session, bg_color=None, silhouettes=None)

Set global parameters. With no options reports the current settings.

Parameters:

bg_color : Color

Set the graphics window background color.

silhouettes : bool

Enable or disable silhouette edges (black lines drawn at boundaries of objects where the depth of the scene jumps.

snav

snav(session, enable=None, fly=None)

Enable or disable moving models with Space Navigator input device.

Parameters:

enable : bool

Enable (true) or disable (false) use of the Space Navigator device.

fly : bool

Enable flying mode where the Space Navigator motions control the camera, for example pushing forward flies the camera forward. If fly is false, then the device controls the models, pushing forward would push the models away from the camera. In both cases it is actually the camera that moves.

split

split(session, molecules=None, chains=None, ligands=False, connected=False, atoms=None)

Split an atomic structure into separate structures, for example one for each chain.

Parameters:

molecules : AtomicStructures

Structures to split.

chains : bool

Split each chain into a separate atomic structure.

ligands : bool

Split each ligand into a separate atomic structure.

connected : bool

Split each connected set of atoms into a separate atomic structure.

atoms : Atoms

Split the specified atoms into a separate atomic structure.

stop

stop(session)

Stop a motion initiated with turn, roll or move with the frames argument.

style

style(session, atom_style, atoms=None)

Set the atom display style.

Parameters:

atom_style : “sphere”, “ball” or “stick”

Controls how atoms and bonds are depicted.

atoms : atom specifier

Change the style of these atoms. If not specified then all atoms are changed.

surface

surface(session, atoms=None, enclose=None, include=None, probe_radius=1.4, grid_spacing=None, resolution=None, level=None, color=None, transparency=None, visible_patches=None, sharp_boundaries=None, nthread=None, replace=True, show=False, hide=False, close=False)

Compute and display solvent excluded molecular surfaces.

Parameters:

atoms : Atoms

Atoms controlling which surface patch is shown. Surfaces are computed for each chain these atoms belong to and patches of these surfaces near the specifed atoms are shown. Solvent, ligands and ions are excluded from each chain surface.

enclose : Atoms

Make a surface enclosing exactly these specified atoms excluding solvent, ligands and ions

include : Atoms

Solvent, ligands or ions to include in the surface.

probe_radius : float

Radius of probe sphere rolled over atoms to produce surface. Only used for solvent excluded surfaces.

grid_spacing : float

Surface is computed on 3-dimensional grid with this spacing between grid points along each axis.

resolution : float

Specifying a resolution value (Angstroms) causes the surface calculation to use a contour surface of a 3-d grid of a sum of Gaussians one centered at each atom instead of a solvent excluded surface. See the molmap command for details.

level : float

Contour level for Gaussian surface in atomic number units. Each Gaussian has height scaled by the atom atomic number.

color : Color

Colors surfaces using this color.

transparency : float

Percentage transparency for surfaces.

visible_patches : int

Maximum number of connected surface pieces per chain to show.

sharp_boundaries : bool

Make the surface triangulation have edges exactly between atoms so per-atom surface colors and surface patches have smoother edges.

nthread : int

Number of CPU threads to use in computing surfaces.

replace : bool

Whether to replace an existing surface for the same atoms or make a copy.

show : bool

Show patches for existing surfaces without computing any new surface.

hide : bool

Undisplay surfaces or patches of surfaces.

close : bool

Close surfaces for the specified atoms.

sym

sym(session, molecules, assembly=None, clear=False, surface_only=False)

Show molecular assemblies of molecular models defined in mmCIF files. These can be subassemblies or symmetrical copies with individual chains placed according to matrices specified in the mmCIF file.

Parameters:

molecules : list of AtomicStructure

List of molecules to show as assemblies.

assembly : string

The name of assembly in the mmCIF file. If this parameter is None then the names of available assemblies are printed in log.

clear : bool

Revert to displaying no assembly, resets the use of any symmetry matrices.

surface_only : bool

Instead of showing instances of the molecule, show instances of surfaces of each chain. The chain surfaces are computed if they do not already exist.

title

Function found in chimera.title.label

title_create(session, name, text='', color=None, size=24, typeface='Arial', xpos=0.5, ypos=0.5, visibility=True)

Create a label at a fixed position in the graphics window.

Parameters:

name : string

Identifier for the label used to change or delete label.

text : string

Displayed text of the label.

color : Color

Color of the label text. If no color is specified black is used on light backgrounds and white is used on dark backgrounds.

size : int

Font size in pixels.

typeface : string

Font name. This must be a true type font installed on Mac in /Library/Fonts and is the name of the font file without the ”.ttf” suffix.

xpos : float

Placement of left edge of text. Range 0 - 1 covers full width of graphics window.

ypos : float

Placement of bottom edge of text. Range 0 - 1 covers full height of graphics window.

visibility : bool

Whether or not to display the label.

title_change(session, name, text=None, color=None, size=None, typeface=None, xpos=None, ypos=None, visibility=None)

Change label parameters.

title_delete(session, name)

Delete label.

toolshed

Function defined in chimera.toolshed.cmd

ts_list(session, tool_type='installed')

List installed tools in the log.

Parameters:

tool_type : string

Types are “installed”, “available”, or “all”

ts_refresh(session, tool_type='installed')

Check for new tools or new tool vesions on server and display them in the tool shed window.

Parameters:

tool_type : string

Types are “installed”, “available”, or “all”

ts_install(session, tool_name, user_only=True, version=None)

Install a tool.

Parameters:

tool_name : string

user_only : bool

Install for this user only, or install for all users.

version : string

ts_remove(session, tool_name)

Remove an installed tool.

Parameters:tool_name : string
ts_start(session, tool_name, *args, **kw)

Start a tool.

Parameters:tool_name : string
ts_update(session, tool_name, version=None)

Update a tool to the latest version.

Parameters:

tool_name : string

version : string

ts_hide(session)

Hide the Tool Shed user interface.

ts_show(session)

Show the Tool Shed user interface.

turn

turn(session, axis=(0, 1, 0), angle=1.5, frames=None)

Rotate the scene. Actually the camera is rotated about the scene center of rotation.

Parameters:

axis : 3 comma-separated numbers

Defines the axis in scene coordinates to rotate about.

angle : float

Rotation angle in degrees.

frames : integer

Repeat the rotation for N frames, typically used in recording movies.

view

view(session)

Move camera so the displayed models fill the graphics window.

volume

volume(session, volumes, style=None, show=None, hide=None, level=None, enclose_volume=None, fast_enclose_volume=None, color=None, brightness=None, transparency=None, step=None, region=None, name_region=None, expand_single_plane=None, origin=None, origin_index=None, voxel_size=None, planes=None, symmetry=None, center=(0, 0, 0), center_index=None, axis=(0, 0, 1), coordinate_system=None, save=None, save_format=None, save_region=None, save_step=None, mask_zone=True, chunk_shapes=None, append=None, compress=None, base_index=1, data_cache_size=None, show_on_open=None, voxel_limit_for_open=None, show_plane=None, voxel_limit_for_plane=None, show_outline_box=None, outline_box_rgb=None, outline_box_linewidth=None, limit_voxel_count=None, voxel_limit=None, color_mode=None, projection_mode=None, bt_correction=None, minimal_texture_memory=None, maximum_intensity_projection=None, linear_interpolation=None, dim_transparency=None, dim_transparent_voxels=None, line_thickness=None, smooth_lines=None, mesh_lighting=None, two_sided_lighting=None, flip_normals=None, subdivide_surface=None, subdivision_levels=None, surface_smoothing=None, smoothing_iterations=None, smoothing_factor=None, square_mesh=None, cap_faces=None, box_faces=None, orthoplanes=None, position_planes=None)

Control the display of density maps.

Parameters:

volumes : list of maps

style : “surface”, “mesh”, or “solid”

show : bool

hide : bool

level : sequence of 1 or 2 floats

In solid style 2 floats are used the first being a density level and second 0-1 brightness value.

enclose_volume : float

fast_enclose_volume : float

color : Color

brightness : float

transparency : float

step : sequence of 3 integers

region : sequence of 6 integers

3 minimum grid indices and 3 maximum grid indices for x,y,z axes.

name_region : string

expand_single_plane : bool

origin : sequence of 3 floats

origin_index : sequence of 3 floats

voxel_size : sequence of 3 floats

planes : not currently supported

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Symmetry assignment options

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symmetry : string

center : string

Parsed as 3 comma-separated floats, or an atom specifier

center_index : sequence of 3 floats

axis : sequence of 3 floats

coordinate_system : not supported, model specifier

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File saving options

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save : string

File name

save_format : string

save_region : sequence of 6 integers

save_step : sequence of 3 integers

mask_zone : bool

chunk_shapes : list of “zyx”, “zxy”, “yxz”, “yzx”, “xzy”, “xyz”

append : bool

compress : bool

base_index : integer

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Global options

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data_cache_size : float

In Mbytes

show_on_open : bool

voxel_limit_for_open : float

show_plane : bool

voxel_limit_for_plane : float

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Rendering options

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show_outline_box : bool

outline_box_rgb : Color

outline_box_linewidth : float

limit_voxel_count : bool

Auto-adjust step size.

voxel_limit : float (Mvoxels)

color_mode : string

Solid rendering pixel formats: ‘auto4’, ‘auto8’, ‘auto12’, ‘auto16’, ‘opaque4’, ‘opaque8’, ‘opaque12’, ‘opaque16’, ‘rgba4’, ‘rgba8’, ‘rgba12’, ‘rgba16’, ‘rgb4’, ‘rgb8’, ‘rgb12’, ‘rgb16’, ‘la4’, ‘la8’, ‘la12’, ‘la16’, ‘l4’, ‘l8’, ‘l12’, ‘l16’

projection_mode : string

One of ‘auto’, ‘2d-xyz’, ‘2d-x’, ‘2d-y’, ‘2d-z’, ‘3d’

bt_correction : bool

Brightness and transparency view angle correction for solid mode.

minimal_texture_memory : bool

Reduce graphics memory use for solid rendering at the expense of rendering speed.

maximum_intensity_projection : bool

linear_interpolation : bool

Interpolate gray levels in solid style rendering.

dim_transparency : bool

Makes transparent surfaces dimmer

dim_transparent_voxels : bool

For solid rendering.

line_thickness : float

smooth_lines : bool

mesh_lighting : bool

two_sided_lighting : bool

flip_normals : bool

subdivide_surface : bool

subdivision_levels : integer

surface_smoothing : bool

smoothing_iterations : integer

smoothing_factor : float

square_mesh : bool

cap_faces : bool

box_faces : bool

orthoplanes : One of ‘xyz’, ‘xy’, ‘xz’, ‘yz’, ‘off’

position_planes : sequence of 3 integers

Intersection grid point of orthoplanes display

vop

vop_add(session, volumes, on_grid=None, bounding_grid=None, subregion='all', step=1, grid_subregion='all', grid_step=1, in_place=False, scale_factors=None, model_id=None)

Add maps.

vop_bin(session, volumes, subregion='all', step=1, bin_size=(2, 2, 2), model_id=None)

Reduce map by averaging over rectangular bins.

vop_boxes(session, volumes, markers, size=0, use_marker_size=False, subregion='all', step=1, model_id=None)

Extract boxes centered at marker positions.

vop_cover(session, volumes, atom_box=None, pad=5.0, box=None, x=None, y=None, z=None, f_box=None, fx=None, fy=None, fz=None, i_box=None, ix=None, iy=None, iz=None, use_symmetry=True, cell_size=None, step=1, model_id=None)

Extend a map using symmetry to cover a specified region.

vop_falloff(session, volumes, iterations=10, in_place=False, subregion='all', step=1, model_id=None)

Smooth edges of a masked map.

vop_flatten(session, volumes, method='multiplyLinear', fitregion=None, subregion='all', step=1, model_id=None)

Make map background flat.

vop_flip(session, volumes, axis='z', subregion='all', step=1, in_place=False, model_id=None)

Flip a map axis reversing the hand.

vop_fourier(session, volumes, subregion='all', step=1, model_id=None, phase=False)

Fourier transform a map

vop_gaussian(session, volumes, s_dev=(1.0, 1.0, 1.0), subregion='all', step=1, value_type=None, model_id=None)

Smooth maps by Gaussian convolution.

vop_laplacian(session, volumes, subregion='all', step=1, model_id=None)

Detect map edges with Laplacian filter.

vop_local_correlation(session, volumes, window_size=5, subtract_mean=False, model_id=None)

Compute correlation between two maps over a sliding window.

vop_maximum(session, volumes, on_grid=None, bounding_grid=None, subregion='all', step=1, grid_subregion='all', grid_step=1, in_place=False, scale_factors=None, model_id=None)

Pointwise maximum of maps.

vop_median(session, volumes, bin_size=3, iterations=1, subregion='all', step=1, model_id=None)

Replace map values with median of neighboring values.

vop_morph(session, volumes, frames=25, start=0, play_step=0.04, play_direction=1, play_range=None, add_mode=False, constant_volume=False, scale_factors=None, hide_original_maps=True, interpolate_colors=True, subregion='all', step=1, model_id=None)

Linearly interpolate pointwise between maps.

vop_multiply(session, volumes, on_grid=None, bounding_grid=None, subregion='all', step=1, grid_subregion='all', grid_step=1, in_place=False, scale_factors=None, model_id=None)

Pointwise multiply maps.

vop_octant(session, volumes, center=None, i_center=None, subregion='all', step=1, in_place=False, fill_value=0, model_id=None)

Extract an octant from a map.

vop_octant_complement(session, volumes, center=None, i_center=None, subregion='all', step=1, in_place=False, fill_value=0, model_id=None)

Zero an octant of a map.

vop_permute_axes(session, volumes, axis_order='xyz', subregion='all', step=1, model_id=None)

Permute map axes.

vop_resample(session, volumes, on_grid=None, bounding_grid=False, subregion='all', step=1, grid_subregion='all', grid_step=1, model_id=None)

Interoplate a map on a new grid.

vop_ridges(session, volumes, level=None, subregion='all', step=1, model_id=None)

Find ridges in a map.

vop_scale(session, volumes, shift=0, factor=1, sd=None, rms=None, value_type=None, type=None, subregion='all', step=1, model_id=None)

Scale, shift and convert number type of map values.

vop_subtract(session, volumes, on_grid=None, bounding_grid=False, subregion='all', step=1, grid_subregion='all', grid_step=1, in_place=False, scale_factors=None, min_rms=False, model_id=None)

Subtract two maps.

vop_threshold(session, volumes, minimum=None, set=None, maximum=None, set_maximum=None, subregion='all', step=1, model_id=None)

Set map values below or above a threshold to a constant.

vop_tile(session, volumes, axis='z', pstep=1, trim=0, columns=None, rows=None, fill_order='ulh', subregion='shown', step=1, model_id=None)

Concatenate maps along an axis.

vop_unbend(session, volumes, path, yaxis, xsize, ysize, grid_spacing=None, subregion='all', step=1, model_id=None)

Unbend a map near a smooth splined path.

vop_unroll(session, volumes, inner_radius=None, outer_radius=None, length=None, grid_spacing=None, axis=(0, 0, 1), center=(0, 0, 0), subregion='all', step=1, model_id=None)

Flatten a cylindrical shell within a map.

vop_zone(session, volumes, atoms=None, radius=None, bond_point_spacing=None, minimal_bounds=False, invert=False, subregion='all', step=1, model_id=None)

Mask a map keeping only parts close to specified atoms.

vseries

vseries_align(session, series, enclose_volume=None, fast_enclose_volume=None)

Align each frame of a map series to the preceeding frame.

vseries_measure(session, series, output=None, centroids=True, color=(0.7, 0.7, 0.7, 1), radius=None)

Report centroid motion of a map series.

vseries_play(session, series, direction='forward', loop=False, max_frame_rate=None, jump_to=None, range=None, start=None, normalize=False, markers=None, preceding_marker_frames=0, following_marker_frames=0, color_range=None, cache_frames=1)

Show a sequence of maps from a volume series.

vseries_save(session, series, path, subregion=None, step=None, value_type=None, threshold=None, zero_mean=False, scale_factor=None, enclose_volume=None, fast_enclose_volume=None, normalize_level=None, align=False, on_grid=None, mask=None, final_value_type=None, compress=False)

Process the frames of a map series and save the result to a a file. Processing can normalize, align, mask and change the numeric value type of maps.

vseries_slider(session, series)

Display a graphical user interface slider to play through frames of a map series.

vseries_stop(session, series)

Stop playing a map series.

wait

wait(session, frames=None)

Wait before proceeding to the next command. Used in movie recording scripts.

Parameters:

frames : integer

Wait until this many frames have been rendered before executing the next command in a command script.