Current ChimeraX Commands

April 24, 2015

Command list obtained using command "help all".

alias [name [text]] [name a text string] [text the rest of line]

buriedarea atoms1 atoms2 [probeRadius a floating point number]

camera [field-of-view [eye-separation [screen-width [depth-scale]]]] [field-of-view a floating point number] [eye-separation a floating point number] [screen-width a floating point number] [depth-scale a floating point number]

ccolor [atoms] [atoms an atom specifier]

celement [atoms] [atoms an atom specifier]

close model-ids

color color [spec] [spec an atom specifier]

colordef name [color] [color a color]

command_line no documentation

contacts [atoms] [probeRadius a floating point number] [atoms an atom specifier]

display [spec] [spec an atom specifier]

dump filename [output] [output a text string]

echo [text] [text the rest of line]

exit

export filename

fitmap atomsOrMap [inMap density map] [metric one of 'overlap', 'correlation', or 'cam'] [envelope a truth value] [resolution a floating point number] [shift a truth value] [rotate a truth value] [symmetric a truth value] [moveWholeMolecules a truth value] [search a whole number] [placement one of 'sr', 's', or 'r'] [radius a floating point number] [clusterAngle a floating point number] [clusterShift a floating point number] [asymmetricUnit a truth value] [inside a floating point number] [sequence a whole number] [maxSteps a whole number] [gridStepMax a floating point number] [gridStepMin a floating point number] [listFits a truth value] [eachModel a truth value]

help [command-name] [command-name a text string]

hide [atoms] [atoms an atom specifier]

lighting [preset] [direction floating point number(s)] [intensity a floating point number] [color a color] [fillDirection floating point number(s)] [fillIntensity a floating point number] [fillColor a color] [ambientIntensity a floating point number] [ambientColor a color] [fixed a truth value] [shadows a truth value] [qualityOfShadows a text string] [depthBias a floating point number] [multiShadow a whole number] [msMapSize a whole number] [msDepthBias a floating point number] [preset one of 'default', 'full', 'soft', 'simple', or 'flat']

list

log no documentation

material [preset] [reflectivity a floating point number] [specularReflectivity a floating point number] [exponent a floating point number] [ambientReflectivity a floating point number] [preset one of 'default', 'shiny', or 'dull']

molmap atoms resolution [gridSpacing a floating point number] [edgePadding a floating point number] [cutoffRange a floating point number] [sigmaFactor a floating point number] [balls a truth value] [displayThreshold a floating point number] [replace a truth value] [showDialog a truth value] oculus enable [panSpeed a floating point number]

open filename [id a model id] [as a text string]

pwd

quit [optional] [optional the rest of line]

sasa [atoms] [probeRadius a floating point number] [atoms an atom specifier]

save filename [width a whole number] [height a whole number] [supersample a whole number] [quality a whole number] [format a text string]

sc [shortcut] [shortcut a text string]

set [bgColor a color] [silhouette a truth value]

show [atoms] [atoms an atom specifier]

snav [enable] [fly a truth value] [enable a truth value]

stop [ignore] [ignore the rest of line]

style atom-style [atoms] [atoms an atom specifier]

surface [atoms] [probeRadius a floating point number] [gridSpacing a floating point number] [color a color] [transparency a floating point number] [chains a truth value] [nthread a whole number] [atoms an atom specifier]

toolshed no documentation

ts [optional] [optional the rest of line]

volume volumes [style one of 'surface', 'mesh', or 'solid'] [show ] [hide ] [level floating point number(s)] [encloseVolume floating point number(s)] [fastEncloseVolume floating point number(s)] [color color(s)] [brightness a floating point number] [transparency a floating point number] [step map step] [region map region] [nameRegion a text string] [expandSinglePlane a truth value] [origin 1 or 3 floats] [originIndex 1 or 3 integers] [voxelSize 1 or 3 floats] [symmetry a text string] [center a text string] [centerIndex 1 or 3 floats] [axis a text string] [save a text string] [saveFormat one of 'mrc', 'cmap', or 'dsn6'] [saveRegion map region] [saveStep 1 or 3 integers] [maskZone a truth value] [chunkShapes collection of one of 'zyx', 'zxy', 'yxz', 'yzx', 'xzy', or 'xyz'] [append a truth value] [compress a truth value] [baseIndex a whole number] [dataCacheSize a floating point number] [showOnOpen a truth value] [voxelLimitForOpen a floating point number] [showPlane a truth value] [voxelLimitForPlane a floating point number] [showOutlineBox a truth value] [outlineBoxRgb a color] [outlineBoxLinewidth a floating point number] [limitVoxelCount a truth value] [voxelLimit a floating point number] [colorMode one of 'auto4', 'auto8', 'auto12', 'auto16', 'opaque4', 'opaque8', 'opaque12', 'opaque16', 'rgba4', 'rgba8', 'rgba12', 'rgba16', 'rgb4', 'rgb8', 'rgb12', 'rgb16', 'la4', 'la8', 'la12', 'la16', 'l4', 'l8', 'l12', or 'l16'] [projectionMode one of 'auto', '2d-xyz', '2d-x', '2d-y', '2d-z', or '3d'] [btCorrection a truth value] [minimalTextureMemory a truth value] [maximumIntensityProjection a truth value] [linearInterpolation a truth value] [dimTransparency a truth value] [dimTransparentVoxels a truth value] [lineThickness a floating point number] [smoothLines a truth value] [meshLighting a truth value] [twoSidedLighting a truth value] [flipNormals a truth value] [subdivideSurface a truth value] [subdivisionLevels a truth value] [surfaceSmoothing a truth value] [smoothingIterations a whole number] [smoothingFactor a floating point number] [squareMesh a truth value] [capFaces a truth value] [boxFaces a truth value] [orthoplanes one of 'xyz', 'xy', 'xz', 'yz', or 'off'] [positionPlanes whole number(s)]

vop add volumes [onGrid density maps] [boundingGrid a truth value] [gridSubregion map region] [gridStep map step] [subregion map region] [step map step] [modelId a model id] [inPlace a truth value] [scaleFactors floating point number(s)]

vop bin volumes [binSize map step] [subregion map region] [step map step] [modelId a model id]

vop boxes volumes markers [size a floating point number] [useMarkerSize a truth value] [subregion map region] [step map step] [modelId a model id]

vop cover volumes [atomBox atoms] [pad a floating point 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 a truth value] [cellSize whole number(s)] [step map step] [modelId a model id]

vop falloff volumes [iterations a whole number] [inPlace a truth value] [subregion map region] [step map step] [modelId a model id]

vop flatten volumes [method one of 'multiplyLinear', or 'divideLinear'] [fitregion map region] [subregion map region] [step map step] [modelId a model id]

vop flip volumes [axis one of 'x', 'y', 'z', 'xy', 'yz', or 'xyz'] [inPlace a truth value] [subregion map region] [step map step] [modelId a model id]

vop fourier volumes [phase a truth value] [subregion map region] [step map step] [modelId a model id]

vop gaussian volumes [sDev 1 or 3 floats] [valueType numeric value type] [subregion map region] [step map step] [modelId a model id]

vop laplacian volumes [subregion map region] [step map step] [modelId a model id]

vop localCorrelation volumes [windowSize a whole number] [subtractMean a truth value] [modelId a model id]

vop maximum volumes [onGrid density maps] [boundingGrid a truth value] [gridSubregion map region] [gridStep map step] [subregion map region] [step map step] [modelId a model id] [inPlace a truth value] [scaleFactors floating point number(s)]

vop median volumes [binSize map step] [iterations a whole number] [subregion map region] [step map step] [modelId a model id]

vop morph volumes [frames a whole number] [start a floating point number] [playStep a floating point number] [playDirection a whole number] [playRange 2 floats] [addMode a truth value] [constantVolume a truth value] [scaleFactors floating point number(s)] [hideOriginalMaps a truth value] [interpolateColors a truth value] [subregion map region] [step map step] [modelId a model id]

vop multiply volumes [onGrid density maps] [boundingGrid a truth value] [gridSubregion map region] [gridStep map step] [subregion map region] [step map step] [modelId a model id] [inPlace a truth value] [scaleFactors floating point number(s)]

vop octant volumes [center floating point number(s)] [iCenter whole number(s)] [fillValue a floating point number] [inPlace a truth value] [subregion map region] [step map step] [modelId a model id]

vop ~octant volumes [center floating point number(s)] [iCenter whole number(s)] [fillValue a floating point number] [inPlace a truth value] [subregion map region] [step map step] [modelId a model id]

vop permuteaxes volumes [axisOrder one of 'xyz', 'xzy', 'yxz', 'yzx', 'zxy', or 'zyx'] [subregion map region] [step map step] [modelId a model id]

vop resample volumes [onGrid density maps] [boundingGrid a truth value] [gridSubregion map region] [gridStep map step] [subregion map region] [step map step] [modelId a model id]

vop ridges volumes [level a floating point number] [subregion map region] [step map step] [modelId a model id]

vop scale volumes [shift a floating point number] [factor a floating point number] [sd a floating point number] [rms a floating point number] [valueType numeric value type] [type numeric value type] [subregion map region] [step map step] [modelId a model id]

vop subtract volumes [onGrid density maps] [boundingGrid a truth value] [gridSubregion map region] [gridStep map step] [subregion map region] [step map step] [modelId a model id] [inPlace a truth value] [scaleFactors floating point number(s)] [minRMS a truth value]

vop threshold volumes [minimum a floating point number] [set a floating point number] [maximum a floating point number] [setMaximum a floating point number] [subregion map region] [step map step] [modelId a model id]

vop tile volumes [axis one of 'x', 'y', or 'z'] [pstep a whole number] [trim a whole number] [columns a whole number] [rows a whole number] [fillOrder one of 'ulh', 'ulv', 'urh', 'urv', 'llh', 'llv', 'lrh', 'lrv', 'ulhr', 'ulvr', 'urhr', 'urvr', 'llhr', 'llvr', 'lrhr', or 'lrvr'] [subregion map region] [step map step] [modelId a model id]

vop unbend volumes path yaxis xsize ysize [gridSpacing a floating point number] [subregion map region] [step map step] [modelId a model id]

vop unroll volumes [innerRadius a floating point number] [outerRadius a floating point number] [length a floating point number] [gridSpacing a floating point number] [axis floating point number(s)] [center floating point number(s)] [subregion map region] [step map step] [modelId a model id]

vop zFlip volumes [axis one of 'x', 'y', 'z', 'xy', 'yz', or 'xyz'] [inPlace a truth value] [subregion map region] [step map step] [modelId a model id]

vop zone volumes atoms radius [bondPointSpacing a floating point number] [minimalBounds a truth value] [invert a truth value] [subregion map region] [step map step] [modelId a model id]

vseries align series [encloseVolume a floating point number] [fastEncloseVolume a floating point number]

vseries measure series [output a text string] [centroids a truth value] [color a color] [radius a floating point number]

vseries play series [loop a truth value] [direction one of 'forward', 'backward', or 'oscillate'] [normalize a truth value] [maxFrameRate a floating point number] [markers atoms] [precedingMarkerFrames a whole number] [followingMarkerFrames a whole number] [colorRange a floating point number] [cacheFrames a whole number] [jumpTo a whole number] [range integer range] [startTime a whole number]

vseries save series path [subregion map region] [step map step] [valueType numeric value type] [threshold a floating point number] [zeroMean a truth value] [scaleFactor a floating point number] [encloseVolume a floating point number] [fastEncloseVolume a floating point number] [normalizeLevel a floating point number] [align a truth value] [onGrid density map] [mask density map] [finalValueType numeric value type] [compress a truth value]

vseries slider series

vseries stop series

window

~alias name

~colordef name

~display [spec] [spec an atom specifier]