Current Chimera 2 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 [maps] [show a truth value] [hide a truth value] [level a floating point number] [step a whole number] [color a color] [transparency a floating point number] [showOutlineBox a truth value] [style one of 'surface', 'mesh', or 'solid']

vseries operation [series] [series map series]

window

~alias name

~colordef name

~display [spec] [spec an atom specifier]