© RasMol v2.6a Quick Reference Card
Copyright 1994 Roger Sayle.[Adapted for this web site by Duane W. Sears]

More comprehensive information on using RasMol can be found in the hypertext version of the RasMol help manual prepared by Eric Martz at the University of Massachusetts.

The most current versions of the RasMol program can be found at internet sites maintained by Roger Sayle in the UK and Eric Martz at the University of Massachusetts.

Index
Rendering Commands Mouse Buttons Manipulation Commands General Commands Set Picking Commands
Atom Expressions Predefined Sets Color Commands Color Schemes Amino Acid Colors
Rendering Commands
Screen ActionCommandArgument
Set background colorbackground<color>
Depth-cueing/lightingset ambient [value]
Enable/disable shadowsset shadows [boolean]
Enable atom highlightsset specular[boolean]
Control atom 'shininess' set specpower[value]
Mouse Buttons[return to Index ]
Moving the mouse while holding mouse buttons and/or control keys manipulates the molecule. The default bindings are described below.
Screen ActionWindows
Mouse button
+ key (pointer on image)		Macintosh
Mouse button
+ key (pointer on image)
popup menuright button, pointer stationarybutton down, pointer stationary
X-rotationleft button, drag button down, drag
Y-rotationleft button, drag button down, drag
Z-rotationright button + Shift key, drag (none)
X-translationright button, + Ctrl key, drag button down, + Option key, drag
Y-translationright button + Ctrl key, drag button down + Option key, drag
zoom inleft button + Shift key, drag button down + Shift key, drag
shrinkleft button + Shift key, drag button down + Shift key, drag
Manipulation Commands [return to Index ]
Screen ActionCommandArgument
Rotate molecule rotate<axis> [-] <value>
Translate molecule translate <axis> [-] <value>
Scale moleculezoom [boolean]
Specify magnificationzoom<value>
Enable/disable slabbingslab[boolean]
Move Z-clipping planeslab<value>
Set center of rotation center[expression]
Reset orientation to default settings resetblank
General Commands[return to Index ]
Screen ActionCommandArgument
Create hard spheres with van der Waals radii for of all of the selected atoms spacefill
= spacefill		(blank)
selected
Create hard spheres with arbitrarily defined radii for of all of the selected atoms; number = 0-700; or turns spacefill off.spacefill<number>
off
Select all atoms of all molecules in the pdb fileselect*
Select all atoms of chain "y"select*y
Display only part of a molecule as defined by the "expression"restrict<expression>
Labels selected items with single amino acid codelabel%m
Labels selected items with triple amino acid code%n
Labels selected items with residue numbers%r
Renders a ribbon trace of the backbone; or turns ribbons off.ribbon(s)<number>
off
Renders a cartoon trace of the backbone with alpha helical ribbons and beta sheet arrowheads pointing in the N-to-C direction; or turns cartoons off.cartoon(s)<number>
off
Renders a line trace of the backbone; or turns trace off.trace<number>
off
Set Picking Commands [return to Index ]
"Set Picking" commands activate the mouse pointer and button for retrieving information from the image.
Note: After issuing the "set picking <value>" command, move the mouse pointer over an atom in the Chime window and click the mouse button (while holding down the Control, Option, or Command keyif using a Macintosh).
Turns "set picking" off thereby inactivating the mouse pointer and button. set pickingnone
An identification label for the atom selected with the mouse is returned to the message box.identify
An identification label for the atom selected with the mouse is placed on the image in the Chime window. label
The distance between 2 atoms sequentially selected with the mouse is returned to the message box. distance
"Monitors" the distance between 2 atoms sequentially selected with the mouse by placing a dashed connecting line on the image in the Chime window along labeled with the distance..monitor(s)
Monitors off" removes all distances and connecting lines shown on the image in the Chime window but does not turn off the distance monitor. (Use the "set picking none" command to accomplish this.)monitor(s)off
The angle defined by 3 atoms sequentially selected with the mouse is returned to the message box.set pickingangle
The torsion angle defined by 4 atoms sequentially selected with the mouse is returned to the message box.torsion
The center of image rotation is changed to the atom selected with the mouse.center
Atom Expressions [return to Index ]
Type of ExpressionExpression
(example)		Comments
Wild Cards:*specifies every atom in the pdb file
as?as? = asp (aspartic acid) plus asn (asparagine)
Predefined Sets:alpha specifies all atoms found within all alpha-helical polypeptdie segments
sheetspecifies all atoms found within all beta-sheet polypeptdie segments
hydrophobicspecifies all atoms in hydrophobic residues
Residue Ranges: 3,16,12 specifies all atoms in residues numbered 3, 16, & 12 in the pdb file
9-20specifies all atoms in residues inclusive of those numbered 9-20
Boolean Operators:backbone and not alpha specifies all atoms defined as part of the backbone but not part of alpha-helical structures
ser90 and *cspecifies all atoms defined as part of serine residue number 90 and also part of the chain "c"
ligand or 196-199 specifies all atoms in residues defined as part of a (nonprotein) ligand and also all atoms comprising residues numbered 196-199
Primitive Expressions:cys, glu, arg
or
(cys, glu, arg)		specifies all atoms in all residues named cys, glu, arg, as? where cys (cysteine), glu (glutaminc acid), and arg (arginine) are 3-letter abbreviations for the standard amino acids
ser70a, **p, glu24:1 specifies all atoms in ser residue 90 in chain "a"plusall atoms in chain "p" plusall atoms in glu residue 24 in chain "l"
hem*p.fe, *.sg specifies only Fe atoms in all hem (heme) ligands in chain "p" plusall atoms in all chains labeled "sg" in the pdb file
Comparison Operators: atomno=4,atomno=6specifies those atoms designated 4 and 6 in the pdb file
temperature>=900 specifies all atoms with a temperature factor greater than or equal to 900
Within Expressions:within (8.0,ligand)specifies all atoms which reside within 8.0 Å distance from any atom defined as part of a ligand
Predefined Sets [return to Index ]
protein setsnucleic acid sets
protein or nucleic acids sets"other molecule/atom"sets
atacidicacyclicaliphaticalphaamino
aromaticbackbonebasicbondedburiedcg
chargedcycliccystinehelixheterohydrogen
hydrophobichohionslarge ligandmedium
neutralnucleicpolarproteinpurinepyrimidine
selectedsheet(s)sidechainsmallsolventsurface
turnwaterUser-defined sets: define <identifier> <expression>
Color Commands [return to Index ]
Color representation:color [object] <color>
Objects: Predefined Colors:Atom Color Schemes:
atomsbondsbackboneblueblack cyangreencpkaminoshapely
ribbon(s)labels hbondsgreenbluemagentaorangepurplegroupchainstructure
ssbondsdots axesredredorangevioletwhitetemperaturechargeuser
cartoon(s)yellow 
Color Schemes[return to Index] Amino Acid Colors
CPK (Corey, Pauling, & Kultun) Atom Colors ASP, GLUbright red[230,10,10]
carbongray[200,200,200]CYS, METyellow[230,230,0]
oxygenred[240,0,0]LYS, ARGblue[20,90,255]
nitrogenlight blue[143,143,255]SER, THRorange[250,150,0]
hydrogenwhite[255,255,255]PHE, TYRmid-blue[50,50,170]
sulfuryellow[255,200,50]ASN, GLNcyan[0,220,220]
phosphorousorange[255,165,0]GLYlight gray[235,235,235]
chlorinegreen[0,255,0]LEU, VAL, ILEgreen[15,130,15]
calcium, metalsdark gray[128,128,144]ALAgray[200,200,200]
unknowndeep pink[255,20,147]TRPpink[180,90,180]
color numerically specified by [R#,G#,B#]
R# = 0-255, G# = 0-255, and B# = 0-255		HISpale blue[130,130,210]
PROflesh[220,150,130]
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© Duane W. Sears
May 7, 1997