wiki:2017-01-09

Version 3 (modified by Tom Goddard, 9 years ago) ( diff )

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Attendees

Conrad, Elaine, Eric, Scooter, TomG, Gregc, Nadya

Agenda

  • Command line

Next week agenda

  • Make ChimeraX wiki public to help outside developers
  • Make a ChimeraX changelog file (Martin Moncrieffe)

Discussion

  • Ready
    • alias
    • buriedarea
    • camera
    • cd
    • close
    • cofr
    • color (but still needs work on sequential)
      • should have "what" option like select
    • colordef
    • colour
    • coordset
    • crossfade
    • delete
    • display (alias for show and hide)
    • dssp
    • echo
    • exit
    • fitmap
    • getcrd
    • hide
    • lighting
    • listinfo
    • log
    • matchmaker
    • material
    • mlp
    • molmap (needs synopsis) -- might want to remove/enhance "balls" option
    • mousemode
    • move
    • movie (subcommands need synopses)
    • open (open formats should be case independent)
    • perframe (needs synopses)
      • Add "perframe stop" and make ~perframe an alias for it
    • pwd
    • quit
    • rainbow
      • Need to implement SSEs, helices, strands
      • May not want volmodel and molmodel, and allmodel
    • rest_server
      • Need to change name to remotecontrol rest
    • ribbon
    • roll
    • save
    • select
      • May want to add "entity atoms" to atom-spec
    • show
      • But "object type" should be "object types"
      • only option may not ready
    • stop
    • struts
    • surface
      • Might add sop subcommands
    • sym
    • time
    • transparency
      • Should say "target object types"
      • Should have "what" option like select
    • turn
    • usage
      • some reformatting would be useful
    • version
    • view
      • May incorporate position and camera
    • volume
    • vr
    • wait
    • windowsize
    • zoom
  • Experimental
    • addmissingatoms
    • align
    • blastprotein (needs to be changed to work in --nogui mode)
    • buriedarea
      • May want to add this to a new measure command
    • cage
    • cartoon except "cartoon param, cartoon scale, and cartoon xsection" are now part of style
    • clip
    • contacts (needs to be changed to work in --nogui mode)
    • crosslinks
    • cytoscape
    • findclash
    • info
    • ks (needs synopsis)
    • pdbimages
    • position
    • remotecontrol
      • But see rest_server above
    • rename
      • Need to design rename and renumber commands that include residues, chains, as well as models
    • resfit
    • run
    • rungs
      • May be replaced by a more complete nucleotide visualization implementation
    • sasa
      • This will become part of the new measure command
    • scolor
      • may be part of color
    • set
      • Issue: options may be in the wrong place
      • Issue: may be absorbed into preference system
    • size
      • May be part of style
    • smoothlines
    • snav
      • May want a device command that adds snav, vr, leap, etc.
    • sop
      • Might want to be part of surface
    • stringdb
    • style
      • Need to discuss how style/cartoon style/size, etc. fit
    • vop
      • Might want to be part of volume
  • In progress
    • 2dlabels
      • Still in progress
      • 2dlabels will certainly be a command, but current syntax will change
      • May just have "2dlabels" and "2dlabels delete"
    • help
      • help URL functionality should move to open URL
      • new_viewer option is strange and should be thought about more carefully
        • May want three options: replace, tab, new window
    • split
    • toolshed
    • vseries
  • Debug
    • dumpspec
    • sdump
    • test
  • Remove
    • list
    • ts
    • vive
  • New commands
    • measure
      • buriedarea
      • sasa
      • distance
      • and others
    • remotecontrol
      • includes xmlrpc and rest
  • Discussion point
    • What should we do about "~"?
    • Think about overlap between view, position, and camera
    • Need to clean up usage hints
    • Need to think about visualization of nucleotides
    • "objects" vs. "atom-spec". Usage separates the two concepts (e.g. see select), but help documentation merges them.
    • Should "entity atoms", which means the same molecular entity, be part of the atom-spec?
    • Need more discussion/revision for select only option
    • Need to discuss style

[no synopsis available] 2dlabels change name [text a text string] [color a color] [size an integer] [typeface a text string] [xpos a number] [ypos a number] [visibility true or false]

name: a label identifier

[no synopsis available] 2dlabels create name [text a text string] [color a color] [size an integer] [typeface a text string] [xpos a number] [ypos a number] [visibility true or false]

name: a text string

[no synopsis available] 2dlabels delete name

name: a label identifier

[no synopsis available] addmissingatoms structures [minimizationSteps an integer] [keepWaters true or false]

structures: atomic structures

define or show a command alias alias name [text]

name: a text string text: the rest of line

remove a command alias alias delete name

name: 'all' or a text string

list aliases alias list [internal] alias of "alias delete $*" ~alias [optional]

optional: the rest of line

Align one set of atoms to another align atoms toAtoms atoms [move one of 'atoms', 'chains', 'molecule atoms', 'molecules', 'nothing', or 'residues'] [each one of 'chain', 'coordset', or 'molecule'] [matchChainIds] [matchSequenceNumbers] [matchAtomNames] [cutoffDistance a number] [reportMatrix]

atoms: atoms

alias of "blastprotein $*" blastpdb [optional]

optional: the rest of line

Search PDB/NR using BLAST blastprotein spec [database one of 'nr' or 'pdb'] [cutoff a number] [matrix one of 'BLOSUM100', 'BLOSUM45', 'BLOSUM62', 'BLOSUM80', 'BLOSUM90', 'PAM30', or 'PAM70'] [maxHits an integer] [log true or false]

spec: an atom specifier

compute buried area buriedarea atoms1 withAtoms2 atoms [probeRadius a number] [listResidues] [cutoffArea a number] [color a color] [select]

atoms1: atoms

Place copies of model on polygons of cage. cage cage [placeModel model] [polygonSides an integer] [surfaceOnly] [resolution a number]

cage: model

adjust camera parameters camera [type] [fieldOfView a number] [eyeSeparation a number] [pixelEyeSeparation a number] [type one of '360', '360sbs', '360tb', 'mono', 'ortho', 'sbs', 'stereo', or 'tb']

type: one of '360', '360sbs', '360tb', 'mono', 'ortho', 'sbs', 'stereo', or 'tb'

undisplay cartoon for specified residues ~cartoon [spec] [spec an atom specifier]

spec: an atom specifier

display cartoon for specified residues cartoon [spec] [smooth a number >= 0.0 and <= 1.0 or 'default'] [style one of 'pandp', 'pipe', 'plank', or 'ribbon'] [hideBackbone true or false] [showSpine true or false] [spec an atom specifier]

spec: an atom specifier

set cartoon style for secondary structures in specified models cartoon style [spec] [width a number] [thickness a number] [arrows true or false] [arrowsHelix true or false] [arrowScale a number >= 1.0 and <= 3.0] [xsection one of 'barbell', 'oval', 'piping', 'rectangle', 'round', or 'square'] [sides an even integer >= 3 and <= 24] [barScale a number] [barSides an even integer >= 3 and <= 24] [ssEnds one of 'default', 'long', or 'short'] [orient one of 'atoms', 'curvature', 'guides', or 'peptide'] [modeHelix one of 'default' or 'tube'] [modeStrand one of 'default' or 'tube'] [spec an atom specifier]

spec: an atom specifier

set cartoon tether options for specified structures cartoon tether [structures] [scale a number >= 0.0 and <= 1.0] [shape one of 'cone', 'cylinder', or 'steeple'] [sides an integer >= 3 and <= 24] [opacity a number >= 0.0 and <= 1.0] [structures atomic structures]

structures: atomic structures

Change the current working directory cd [directory] [directory file name]

directory: file name

set clip planes clip [near 'off' or a number] [far 'off' or a number] [front 'off' or a number] [back 'off' or a number] [list] [off] [position center point] [axis an axis vector] [coordinateSystem a coordinate-system] alias of "clip off" ~clip close models close [models] [models models]

models: models

set center of rotation method cofr [method [objects [pivot]]] [coordinateSystem model] [method one of 'fixed', 'front center', or 'frontCenter' or nothing] [objects objects or nothing] [pivot some numbers]

method: one of 'fixed', 'front center', or 'frontCenter' or nothing objects: objects or nothing pivot: some numbers

set center of rotation method to front center ~cofr color objects color objects [color [what]] [target a text string] [transparency a number] [sequential one of 'SSEs', 'allmodels', 'chains', 'entities', 'helices', 'helix', 'molmodels', 'residues', 'strands', or 'volmodels'] [halfbond true or false] [map density map] [palette a colormap] [range some numbers or 'full'] [offset a number] [color a color or one of 'byatom', 'bychain', 'byelement', 'byentity', 'byhetero', 'bymodel', 'fromatoms', or 'random'] [what one of 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', or 'surfaces']

objects: objects or nothing color: a color or one of 'byatom', 'bychain', 'byelement', 'byentity', 'byhetero', 'bymodel', 'fromatoms', or 'random' what: one of 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', or 'surfaces'

remove color definition color delete name

name: 'all' or a text string

list colors color list [all] name a custom color color name name color

name: a text string color: a color

show color color show name

name: the rest of line

alias of "color name $*" colordef [optional]

optional: the rest of line

alias of "color delete $*" ~colordef [optional]

optional: the rest of line

alias of "color $*" colour [optional]

optional: the rest of line

[no synopsis available] contacts [atoms] [probeRadius a number] [areaCutoff a number] [interfaceResidueAreaCutoff a number] [atoms atoms]

atoms: atoms

show coordinate sets coordset molecules indexRange [holdSteady atoms] [loop an integer]

molecules: atomic structures indexRange: some integers

Fade between one rendered scene and the next scene. crossfade [frames] [frames an integer >= 1]

frames: an integer >= 1

Plot or minimize crosslink lengths crosslinks pbonds [color a color] [radius a number] [network] [plot] [ensemble structure] [minimize structures] [iterations an integer] [frames an integer]

pbonds: pseudobonds

Connect to Cytoscape cytoscape connect [port an integer] Connect to Cytoscape cytoscape send [arguments] [namespace a text string] [command a text string] [arguments the rest of line]

arguments: the rest of line

delete atoms delete atoms

atoms: atoms

alias of "hide $*" ~display [optional]

optional: the rest of line

alias of "show $*" display [optional]

optional: the rest of line

compute/assign secondary structure using Kabsch & Sander DSSP algorithm dssp [structures] [minHelixLen an integer] [minStrandLen an integer] [energyCutoff a number] [report true or false] [structures structures]

structures: structures

report what an atom specifier matches dumpspec spec

spec: an atom specifier

alias of "log text $*" echo [optional]

optional: the rest of line

exit application exit find clashes between atom pairs findclash spec [makePseudobonds true or false] [log true or false] [namingStyle one of 'command', 'command-line', 'serial', 'serialnumber', or 'simple'] [overlapCutoff a number] [hbondAllowance a number] [bondSeparation an integer] [test one of 'model', 'other', or 'self' or an atom specifier] [intraResidue true or false]

spec: an atom specifier

[no synopsis available] fitmap atomsOrMap inMap density map [subtractMaps objects] [eachModel true or false] [sequence an integer] [search an integer] [metric one of 'cam', 'correlation', or 'overlap'] [envelope true or false] [resolution a number] [shift true or false] [rotate true or false] [symmetric true or false] [maxSteps an integer] [gridStepMax a number] [gridStepMin a number] [placement one of 'r', 's', or 'sr'] [radius a number] [clusterAngle a number] [clusterShift a number] [asymmetricUnit true or false] [levelInside a number] [moveWholeMolecules true or false] [listFits true or false]

atomsOrMap: objects

report atomic coordinates getcrd spec [coordinateSystem] [coordinateSystem one of 'model', 'scene', or 'screen']

spec: an atom specifier coordinateSystem: one of 'model', 'scene', or 'screen'

display help help [topic]

topic: the rest of line

hide specified objects hide [objects [what]] [target object type] [objects objects or nothing] [what one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces']

objects: objects or nothing what: one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'

report info about models info [models] [models models]

models: models

[no synopsis available] ks [shortcut] [shortcut a text string]

shortcut: a text string

report or alter lighting parameters lighting [preset] [direction some numbers] [intensity a number] [color a color] [fillDirection some numbers] [fillIntensity a number] [fillColor a color] [ambientIntensity a number] [ambientColor a color] [depthCue true or false] [depthCueStart a number] [depthCueEnd a number] [depthCueColor a color] [moveWithCamera true or false] [shadows true or false] [qualityOfShadows a text string] [depthBias a number] [multiShadow an integer] [msMapSize an integer] [msDepthBias a number] [preset one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft']

preset: one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft'

list open model ids list Report atom information listinfo atoms spec [attribute a text string]

spec: an atom specifier or nothing

Report chain information listinfo chains spec [attribute a text string]

spec: an atom specifier or nothing

Report distance matrix information listinfo distmat spec

spec: an atom specifier or nothing

Report model information listinfo models spec [type a text string] [attribute a text string]

spec: an atom specifier or nothing

Resume notifications listinfo notify resume what clientId

what: one of 'models' or 'selection' clientId: a text string

Start notifications for events listinfo notify start what clientId [prefix a text string] [url a text string]

what: one of 'models' or 'selection' clientId: a text string

Stop notifications for events listinfo notify stop what clientId

what: one of 'models' or 'selection' clientId: a text string

Suspend notifications listinfo notify suspend what clientId

what: one of 'models' or 'selection' clientId: a text string

Report polymer information listinfo polymers spec

spec: an atom specifier or nothing

Report residue attribute information listinfo resattr Report residue information listinfo residues spec [attribute a text string]

spec: an atom specifier or nothing

Report selection information listinfo selection [level one of 'atom', 'chain', 'model', 'molecule', or 'residue'] [mode one of 'all' or 'any'] [attribute a text string] [no synopsis available] log [show] [hide] [clear] [thumbnail] [text the rest of line] [html the rest of line] [width an integer] [height an integer] [savePath file name] [warningDialog true or false] [errorDialog true or false] [no synopsis available] matchmaker matchAtoms to atoms [pairing a text string] [alg a text string] [verbose true or false] [ssFraction a number or true or false] [matrix a text string] [gapOpen a number] [hgap a number] [sgap a number] [ogap a number] [iterate a number or true or false] [gapExtend a number] [bring atoms] [showAlignment true or false] [computeSs true or false] [matHh a number] [matSs a number] [matOo a number] [matHs a number] [matHo a number] [matSo a number]

matchAtoms: atoms

report or alter material parameters material [preset] [reflectivity a number] [specularReflectivity a number] [exponent a number] [ambientReflectivity a number] [transparentCastShadows true or false] [preset one of 'default', 'dull', or 'shiny']

preset: one of 'default', 'dull', or 'shiny'

display molecular lipophilic potential for selected models mlp [atoms] [spacing a number] [maxDistance a number] [method one of 'brasseur', 'buckingham', 'dubost', 'fauchere', or 'type5'] [nexp a number] [color true or false] [palette a colormap] [range some numbers or 'full'] [map] [atoms atoms]

atoms: atoms

alias of "matchmaker $*" mmaker [optional]

optional: the rest of line

[no synopsis available] molmap atoms resolution [gridSpacing a number] [edgePadding a number] [onGrid density map] [cutoffRange a number] [sigmaFactor a number] [balls true or false] [symmetry symmetry] [center center point] [axis an axis vector] [coordinateSystem a coordinate-system] [displayThreshold a number] [replace true or false] [showDialog true or false]

atoms: atoms resolution: a number

set mouse mode mousemode [leftMode one of 'select', 'select add', 'select subtract', 'select toggle', 'rotate', 'translate', 'zoom', 'rotate and select', 'translate selected models', 'rotate selected models', 'clip', 'clip rotate', 'identify object', 'pivot', 'contour level', 'move planes', 'place marker', 'mark centroid', 'connect markers', 'play map series', 'none', 'tug'] [middleMode one of 'select', 'select add', 'select subtract', 'select toggle', 'rotate', 'translate', 'zoom', 'rotate and select', 'translate selected models', 'rotate selected models', 'clip', 'clip rotate', 'identify object', 'pivot', 'contour level', 'move planes', 'place marker', 'mark centroid', 'connect markers', 'play map series', 'none', 'tug'] [rightMode one of 'select', 'select add', 'select subtract', 'select toggle', 'rotate', 'translate', 'zoom', 'rotate and select', 'translate selected models', 'rotate selected models', 'clip', 'clip rotate', 'identify object', 'pivot', 'contour level', 'move planes', 'place marker', 'mark centroid', 'connect markers', 'play map series', 'none', 'tug'] [wheelMode one of 'select', 'select add', 'select subtract', 'select toggle', 'rotate', 'translate', 'zoom', 'rotate and select', 'translate selected models', 'rotate selected models', 'clip', 'clip rotate', 'identify object', 'pivot', 'contour level', 'move planes', 'place marker', 'mark centroid', 'connect markers', 'play map series', 'none', 'tug'] [pauseMode one of 'select', 'select add', 'select subtract', 'select toggle', 'rotate', 'translate', 'zoom', 'rotate and select', 'translate selected models', 'rotate selected models', 'clip', 'clip rotate', 'identify object', 'pivot', 'contour level', 'move planes', 'place marker', 'mark centroid', 'connect markers', 'play map series', 'none', 'tug'] [alt] [command] [control] [shift] move camera, models, or atoms move axis [distance [frames]] [coordinateSystem a coordinate-system] [models top models] [atoms atoms] [distance a number] [frames an integer >= 1]

axis: an axis vector distance: a number frames: an integer >= 1

[no synopsis available] movie abort [no synopsis available] movie crossfade [frames] [frames an integer]

frames: an integer

[no synopsis available] movie duplicate [frames] [frames an integer]

frames: an integer

[no synopsis available] movie encode [output] [format one of 'avi', 'h264', 'mov', 'qt', 'quicktime', or 'wmv'] [quality one of 'fair', 'good', 'high', 'higher', 'highest', 'low', or 'medium'] [qscale an integer] [bitrate a number] [framerate a number] [resetMode one of 'clear', 'keep', or 'none'] [roundTrip true or false] [wait true or false] [verbose true or false] [output some file names]

output: some file names

[no synopsis available] movie formats [no synopsis available] movie ignore [ignore] [ignore true or false]

ignore: true or false

[no synopsis available] movie record [directory file name] [pattern a text string] [format one of 'JPEG', 'PNG', or 'PPM'] [size some integers] [supersample an integer] [limit an integer] [no synopsis available] movie reset [resetMode] [resetMode one of 'clear', 'keep', or 'none']

resetMode: one of 'clear', 'keep', or 'none'

[no synopsis available] movie status [no synopsis available] movie stop read and display data open filename [format one of 'apbs', 'binary coordinates', 'bmp', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'dsn6', 'dsn6', 'fasta', 'gif', 'html', 'ihm', 'images', 'jpeg', 'mmcif', 'mmtf', 'mrc', 'msf', 'pdb', 'png', 'ppm', 'pseudobonds', 'py', 'session', 'stl', 'storm', 'tiff', 'vtk', 'x3d'] [name a text string] [fromDatabase one of 'cellpack', 'eds', 'edsdiff', 'emdb', 'pdb', 'pdbe', 'pdbe_updated', 'pdbj'] [ignoreCache] [smartInitialDisplay true or false] [trajectory] [series true or false] [oneAlignment true or false] [autoAssociate true or false] [model model]

filename: file name

report formats that can be opened open formats Render mmCIF assembly images pdbimages [directory] [width an integer] [height an integer] [supersample an integer] [imageSuffix a text string] [exclude some text strings] [logFile a text string] [directory file name]

directory: file name

[no synopsis available] perframe command [ranges a range, repeatable] [frames an integer] [interval an integer] [format a text string] [zeroPadWidth an integer] [showCommands]

command: a text string

[no synopsis available] ~perframe set camera and model positions position [camera a position] [models model positions] [coordinateSystem a coordinate-system] set models to initial positions position initial [models] [models models]

models: models

print current working directory pwd alias of "exit $*" quit [optional]

optional: the rest of line

color residues and chains sequentially rainbow objects [level] [target a text string] [transparency a number] [palette a colormap] [halfbond true or false] [level one of 'SSEs', 'allmodels', 'chains', 'entities', 'helices', 'helix', 'molmodels', 'residues', 'strands', or 'volmodels']

objects: objects or nothing level: one of 'SSEs', 'allmodels', 'chains', 'entities', 'helices', 'helix', 'molmodels', 'residues', 'strands', or 'volmodels'

Allow other processes to send commands to ChimeraX remotecontrol enable [address a text string] [port an integer] [timeout a number]

enable: true or false

rename a model or change its id number rename models [name] [id a model id] [name a text string]

models: top models name: a text string

Display slider to show fit of each residue in density map resfit atoms [map density map] [residueRange some integers] [motionFrames an integer] [pauseFrames an integer] [movieFramerate an integer]

atoms: atoms

Report REST server port rest_server port Start REST server rest_server start [port an integer] [ssl true or false] Stop REST server rest_server stop [quiet] alias of "cartoon $*" ribbon [optional]

optional: the rest of line

alias of "~cartoon $*" ~ribbon [optional]

optional: the rest of line

rotate models continuously roll [axis [angle [frames]]] [center center point] [coordinateSystem a coordinate-system] [rock an integer >= 1] [models top models] [atoms atoms] [axis an axis vector] [angle a number] [frames an integer >= 1]

axis: an axis vector angle: a number frames: an integer >= 1

indirectly run a command run text [log [downgradeErrors]] [log true or false] [downgradeErrors true or false]

text: a text string log: true or false downgradeErrors: true or false

depict nucleic acid residues as cylinders rungs [atoms [color [radius [halfbond [hide [hideAtoms [showRibbon [hideHbonds]]]]]]]] [atoms atoms] [color a color] [radius a number] [halfbond true or false] [hide] [hideAtoms true or false] [showRibbon true or false] [hideHbonds true or false]

atoms: atoms color: a color radius: a number halfbond: true or false hide: nothing hideAtoms: true or false showRibbon: true or false hideHbonds: true or false

compute solvent accessible surface area sasa [atoms] [probeRadius a number] [sum atoms] [atoms atoms]

atoms: atoms

save session or image save filename [models] [format one of 'binary coordinates', 'bmp', 'cmap', 'dsn6', 'gif', 'jpeg', 'mmcif', 'mrc', 'png', 'ppm', 'session', 'stl', 'tiff', 'x3d'] [width an integer >= 1] [height an integer >= 1] [supersample an integer >= 1] [pixelSize a number] [transparentBackground] [quality an integer >= 0 and <= 100] [region map region] [step 1 or 3 integers] [maskZone] [chunkShapes a collection of one of 'xyz', 'xzy', 'yxz', 'yzx', 'zxy', or 'zyx'] [append] [compress] [baseIndex an integer] [models models]

filename: file name models: models

report formats that can be saved save formats save image save image filename [format one of 'bmp', 'gif', 'jpeg', 'png', 'ppm', 'tiff'] [width an integer >= 1] [height an integer >= 1] [supersample an integer >= 1] [pixelSize a number] [transparentBackground] [quality an integer >= 0 and <= 100]

filename: file name

save map save map filename [models] [format one of 'cmap', 'dsn6', 'mrc'] [region map region] [step 1 or 3 integers] [maskZone] [chunkShapes a collection of one of 'xyz', 'xzy', 'yxz', 'yzx', 'zxy', or 'zyx'] [append] [compress] [baseIndex an integer] [models models]

filename: file name models: models

save session save session filename

filename: file name

color surfaces scolor [atoms [color]] [opacity an integer] [byatom] [map density map] [palette a colormap] [range some numbers or 'full'] [offset a number] [atoms atoms or nothing] [color a color]

atoms: atoms or nothing color: a color

create human-readable session sdump sessionFile [output] [output file name]

sessionFile: file name output: file name

select specified objects select [objects] [add objects] [subtract objects] [intersect objects] [entity atoms] [clear] [objects objects]

objects: objects

add objects to selection select add [objects] [objects objects]

objects: objects

clear the selection select clear intersect objects with selection select intersect objects

objects: objects

subtract objects from selection select subtract [objects] [objects objects]

objects: objects

alias of "select subtract $*" ~select [optional]

optional: the rest of line

set preferences set [bgColor a color] [silhouettes true or false] [silhouetteWidth a number] [silhouetteColor a color] [silhouetteDepthJump a number] [subdivision a number] alias of "hide $*" ~show [optional]

optional: the rest of line

show specified objects show [objects [what]] [target object type] [only] [objects objects or nothing] [what one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces']

objects: objects or nothing what: one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'

change atom or bond radii size [objects] [atomRadius 'default' or a number] [stickRadius a number] [objects objects]

objects: objects

[no synopsis available] smoothlines models [stepFactor a number] [iterations an integer] [replace]

models: models

[no synopsis available] snav [enable] [fly true or false] [enable true or false]

enable: true or false

hide small connected surface patches sop dust surfaces [metric one of 'area', 'area rank', 'size', 'size rank', 'volume', or 'volume rank'] [size a number] [update true or false]

surfaces: surfaces

show surface near atoms sop zone surfaces nearAtoms atoms [range a number] [bondPointSpacing a number] [maxComponents an integer] [update true or false]

surfaces: surfaces

split molecule into multiple molecules split [molecules] [chains] [ligands] [connected] [atoms atoms] [molecules structures]

molecules: structures

stop all motion stop Load interaction partners from string-db stringdb [structures] [species a text string] [cutoff a number] [partners an integer] [structures atomic structures]

structures: atomic structures

[no synopsis available] struts atoms [length a number] [loop a number] [radius a number] [color a color] [fattenRibbon true or false] [replace true or false] [name a text string] [modelId a model id]

atoms: atoms

[no synopsis available] struts delete [atoms] [atoms atoms]

atoms: atoms

change atom and bond depiction style objects [atomStyle [dashes]] [atomStyle one of 'ball', 'sphere', or 'stick'] [dashes an integer]

objects: objects or nothing atomStyle: one of 'ball', 'sphere', or 'stick' dashes: an integer

create molecular surface surface [atoms] [enclose atoms] [include atoms] [probeRadius a number] [gridSpacing a number] [resolution a number] [level a number] [color a color] [transparency a number] [visiblePatches an integer] [sharpBoundaries true or false] [nthread an integer] [replace true or false] [show] [hide] [close] [atoms atoms]

atoms: atoms

hide molecular surface ~surface [atoms] [atoms atoms]

atoms: atoms

create model copies sym molecules [symmetry] [center center point] [axis an axis vector] [coordinateSystem a coordinate-system] [assembly a text string] [copies] [clear] [surfaceOnly] [resolution a number] [gridSpacing a number] [symmetry symmetry]

molecules: atomic structures symmetry: symmetry

Run through test sequence of commands to check for errors test time a command time command

command: the rest of line

Hide tool from view toolshed hide toolName

toolName: a text string

[no synopsis available] toolshed install bundleName [userOnly [version]] [userOnly true or false] [version a text string]

bundleName: a text string userOnly: true or false version: a text string

[no synopsis available] toolshed list [bundleType]

bundleType: one of 'all', 'available', or 'installed'

[no synopsis available] toolshed refresh [bundleType] [bundleType one of 'all', 'available', or 'installed']

bundleType: one of 'all', 'available', or 'installed'

[no synopsis available] toolshed remove bundleName

bundleName: a text string

Show tool. Start if necessary toolshed show toolName

toolName: a text string

change object transparency transparency objects percent [target a text string]

objects: objects or nothing percent: a number

alias of "toolshed $*" ts [optional]

optional: the rest of line

rotate models turn [axis [angle [frames]]] [center center point] [coordinateSystem a coordinate-system] [rock an integer >= 1] [models top models] [atoms atoms] [axis an axis vector] [angle a number] [frames an integer >= 1]

axis: an axis vector angle: a number frames: an integer >= 1

show command usage usage [commandName]

commandName: the rest of line

show version information version [format]

format: one of 'bundles', 'packages', or 'verbose'

adjust camera so everything is visible view [objects [frames]] [clip true or false] [cofr true or false] [orient] [pad a number] [objects objects or a view name] [frames an integer >= 1]

objects: objects or a view name frames: an integer >= 1

delete named view view delete name

name: a text string

list named views view list save view with name view name name

name: a text string

Start SteamVR virtual reality rendering vive enable

enable: true or false

[no synopsis available] volume volumes [style one of 'mesh', 'solid', or 'surface'] [show] [hide] [toggle] [level some numbers, repeatable] [rmsLevel some numbers, repeatable] [sdLevel some numbers, repeatable] [encloseVolume some numbers] [fastEncloseVolume some numbers] [color a color, repeatable] [brightness a number] [transparency a number] [step map step] [region map region] [nameRegion a text string] [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3 floats] [voxelSize 1 or 3 floats] [planes planes x|y|z,<start>[,<end>[,<increment>[,<depth>]]]] [dumpHeader] [symmetry symmetry] [center center point] [centerIndex 1 or 3 floats] [axis an axis vector] [coordinateSystem a coordinate-system] [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a number] [showOutlineBox true or false] [outlineBoxRgb a color] [outlineBoxLinewidth a number] [limitVoxelCount true or false] [voxelLimit a number] [colorMode one of 'auto12', 'auto16', 'auto4', 'auto8', 'l12', 'l16', 'l4', 'l8', 'la12', 'la16', 'la4', 'la8', 'opaque12', 'opaque16', 'opaque4', 'opaque8', 'rgb12', 'rgb16', 'rgb4', 'rgb8', 'rgba12', 'rgba16', 'rgba4', or 'rgba8'] [projectionMode one of '2d-x', '2d-xyz', '2d-y', '2d-z', '3d', or 'auto'] [btCorrection true or false] [minimalTextureMemory true or false] [maximumIntensityProjection true or false] [linearInterpolation true or false] [dimTransparency true or false] [dimTransparentVoxels true or false] [lineThickness a number] [smoothLines true or false] [meshLighting true or false] [twoSidedLighting true or false] [flipNormals true or false] [subdivideSurface true or false] [subdivisionLevels an integer] [surfaceSmoothing true or false] [smoothingIterations an integer] [smoothingFactor a number] [squareMesh true or false] [capFaces true or false] [boxFaces true or false] [orthoplanes one of 'off', 'xy', 'xyz', 'xz', or 'yz'] [positionPlanes some integers]

volumes: density maps

[no synopsis available] vop add volumes [onGrid density maps] [boundingGrid true or false] [gridSubregion map region] [gridStep map step] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id] [inPlace true or false] [scaleFactors some numbers]

volumes: density maps

[no synopsis available] vop bin volumes [binSize map step] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop boxes volumes centers atoms [size a number] [isize an integer] [useMarkerSize true or false] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop cover volumes [atomBox atoms] [pad a number] [box box bounds] [x 2 floats] [y 2 floats] [z 2 floats] [fbox box bounds] [fx 2 floats] [fy 2 floats] [fz 2 floats] [ibox box bounds] [ix 2 floats] [iy 2 floats] [iz 2 floats] [useSymmetry true or false] [cellSize some integers] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop falloff volumes [iterations an integer] [inPlace true or false] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop flatten volumes [method one of 'divideLinear' or 'multiplyLinear'] [fitregion map region] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop flip volumes [axis one of 'x', 'xy', 'xyz', 'y', 'yz', or 'z'] [inPlace true or false] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop fourier volumes [phase true or false] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop gaussian volumes [sDev 1 or 3 floats] [valueType numeric value type] [invert] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop laplacian volumes [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop localCorrelation volumes [windowSize an integer] [subtractMean] [modelId a model id]

volumes: density maps

[no synopsis available] vop maximum volumes [onGrid density maps] [boundingGrid true or false] [gridSubregion map region] [gridStep map step] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id] [inPlace true or false] [scaleFactors some numbers]

volumes: density maps

[no synopsis available] vop median volumes [binSize map step] [iterations an integer] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop minimum volumes [onGrid density maps] [boundingGrid true or false] [gridSubregion map region] [gridStep map step] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id] [inPlace true or false] [scaleFactors some numbers]

volumes: density maps

[no synopsis available] vop morph volumes [frames an integer] [start a number] [playStep a number] [playDirection an integer] [playRange 2 floats] [addMode true or false] [constantVolume true or false] [scaleFactors some numbers] [hideOriginalMaps true or false] [interpolateColors true or false] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop multiply volumes [onGrid density maps] [boundingGrid true or false] [gridSubregion map region] [gridStep map step] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id] [inPlace true or false] [scaleFactors some numbers]

volumes: density maps

[no synopsis available] vop new [name] [size 1 or 3 integers] [gridSpacing 1 or 3 floats] [origin some numbers] [cellAngles 1 or 3 floats] [valueType numeric value type] [modelId a model id] [name a text string]

name: a text string

[no synopsis available] vop octant volumes [center some numbers] [iCenter some integers] [fillValue a number] [inPlace true or false] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop ~octant volumes [center some numbers] [iCenter some integers] [fillValue a number] [inPlace true or false] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop permuteAxes volumes axisOrder [subregion map region] [step map step] [modelId a model id]

volumes: density maps axisOrder: one of 'xyz', 'xzy', 'yxz', 'yzx', 'zxy', or 'zyx'

[no synopsis available] vop resample volumes onGrid density maps [boundingGrid true or false] [gridSubregion map region] [gridStep map step] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop ridges volumes [level a number] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop scale volumes [shift a number] [factor a number] [sd a number] [rms a number] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop subtract volumes [onGrid density maps] [boundingGrid true or false] [gridSubregion map region] [gridStep map step] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id] [inPlace true or false] [scaleFactors some numbers] [minRms]

volumes: density maps

[no synopsis available] vop threshold volumes [minimum a number] [set a number] [maximum a number] [setMaximum a number] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop tile volumes [axis one of 'x', 'y', or 'z'] [pstep an integer] [trim an integer] [columns an integer] [rows an integer] [fillOrder one of 'llh', 'llhr', 'llv', 'llvr', 'lrh', 'lrhr', 'lrv', 'lrvr', 'ulh', 'ulhr', 'ulv', 'ulvr', 'urh', 'urhr', 'urv', or 'urvr'] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop unbend volumes path atoms [yaxis an axis vector] [xsize a number] [ysize a number] [gridSpacing a number] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop unroll volumes [innerRadius a number] [outerRadius a number] [length a number] [gridSpacing a number] [axis an axis vector] [center center point] [coordinateSystem a coordinate-system] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

[no synopsis available] vop zone volumes nearAtoms atoms range a number [bondPointSpacing a number] [minimalBounds] [invert] [subregion map region] [step map step] [modelId a model id]

volumes: density maps

Start SteamVR virtual reality rendering vr enable

enable: true or false

[no synopsis available] vseries align series [encloseVolume a number] [fastEncloseVolume a number]

series: map series

[no synopsis available] vseries measure series [output a text string] [centroids true or false] [color a color] [radius a number]

series: map series

[no synopsis available] vseries play series [loop true or false] [direction one of 'backward', 'forward', or 'oscillate'] [normalize true or false] [maxFrameRate a number] [pauseFrames an integer] [markers atoms] [precedingMarkerFrames an integer] [followingMarkerFrames an integer] [colorRange a number] [cacheFrames an integer] [jumpTo an integer] [range integer range] [startTime an integer]

series: map series

[no synopsis available] vseries save series path [subregion map region] [step map step] [valueType numeric value type] [threshold a number] [zeroMean true or false] [scaleFactor a number] [encloseVolume a number] [fastEncloseVolume a number] [normalizeLevel a number] [align true or false] [onGrid density map] [mask density map] [finalValueType numeric value type] [compress true or false]

series: map series path: a text string

[no synopsis available] vseries slider series

series: map series

[no synopsis available] vseries stop series

series: map series

suspend command processing for a specified number of frames or until finite motions have stopped wait [frames] [frames an integer >= 1]

frames: an integer >= 1

report or set window size windowsize [width [height]] [width an integer >= 1] [height an integer >= 1]

width: an integer >= 1 height: an integer >= 1

zoom models zoom factor [frames] [frames an integer >= 1]

factor: a number frames: an integer >= 1

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