Changes between Version 1 and Version 2 of 2017-01-09

Timestamp:

Jan 9, 2017, 1:53:37 PM (9 years ago)

Author:

Scooter Morris

Comment:

--

2017-01-09

@@ -15 +15 @@
   * cofr
   * color (but still needs work on sequential)
+   * should have "what" option like select
   * colordef
   * colour
@@ -40 +41 @@
   * 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
@@ -50 +88 @@
   * crosslinks
   * cytoscape
-  * dumpspec
   * 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
@@ -64 +129 @@
    * 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