RasMol v2.7.1
Quick Reference Card
©Copyright Roger Sayle 1992-1999
V2.6x1 Mods ©Copyright Arne Mueller1998
V2.7.1 ©Copyright Herbert J. Bernstein 1998-1999
Mouse Buttons
Clicking on an atom identifies that atom in the command
window. Moving the mouse whilst holding mouse buttons
and/or control keys manipulates the molecule. The default
bindings are described below.
Mac
--Command
Shift
Shift-Cmnd
Control
Windows
Left
Right
Shift Left
Shift Right
Control Left
Action
Rotate X-Y
Translate X-Y
Zoom
Rotate Z
Z-Clipping (Slab)
General Commands
load [format] <filename> Load a molecule
pdb
Brookhaven Protein Databank
mdl
Molecular Design Limited's Mol file
mol2
Tripos' Sybyl Mol2 file format
alchemy Tripos' Alchemy file format
charmm CHARMm format card file
xyz
MSC's XMOL XYZ file format
mopac
J.P. Stewart's MOPAC file format
cif
IUCr CIF or mmCIF file format
exit
quit
Exit from RasMol Script
Terminate pgm execution
help [topic [subtopic]] Display on-line help topic
select <expression>
restrict <expression>
Update part of molecule
Display only part of mol.
set bondmode [mode]
Change bond selection
script <filename>
Execute file of commands
zap
Delete molecule
Display Commands
Colour Commands
wireframe [boolean] Display wireframe
wireframe <value>
Display stick bonds
set bondmode all
Mark all atoms
set bondmode none
Mark no atoms
set bondmode not bonded
Mark non-bonded atoms
colour [object] <colour>
spacefill [boolean]
Display spacefill spheres
spacefill <value>
Specify atom sphere radius
spacefill temperature
spacefill user
star ...
Display stars for spheres
backbone [boolean]
backbone <value>
Display alpha backbone
Specify backbone radius
ribbons [boolean]
ribbons <value>
Display solid ribbons
Specify ribbon width
strands [boolean]
strands <value>
set strands <value>
Draw ribbon as strands
Specify ribbon width
Number of ribbon strands
label [boolean]
Draw default atom labels
label <string>
Label with arbitrary text
set fontsize <value> [FS|PS]
Set label font height
set fontstroke<value> Set label stroke width
ssbonds [boolean]
ssbonds <value>
set ssbonds backbone
set ssbonds sidechain
Display disulphide bonds
Specify ssbond radius
SSBonds between alphas
SSBonds between sulphurs
hbonds [boolean]
hbonds <value>
set hbonds backbone
set hbonds sidechain
Display hydrogen bonds
Specify hbond radius
HBonds between alphas
HBonds donor/acceptor
dots [boolean]
dots <value>
Display dot surface
Specify dot density
set solvent [boolean]
set radius <value>
VDW or solvent surface
Specify probe sphere rad.
Objects:
atoms
ribbons
ssbonds
ribbons1
Colour representation
bonds
labels
dots
ribbons2
Predefined Colours:
Black
Blue
Cyan
Gold
GreenBlue GreenTint
Orange
Pink
Red
RedOrange
Violet
White
BlueTint
Grey
HotPink
PinkTint
SeaGreen
Yellow
Atom Colour Schemes:
cpk
amino
group
chain
temperature
charge
alt
model
colour hbonds type
colour dots potential
backbone
hbonds
axes
Brown
Green
Magenta
Purple
SkyBlue
YellowTont
shapely
structure
user
Colour hbonds by offset
Display potential surface
Manipulation Commands
rotate <axis> [-] <value> Rotate molecule
translate <axis> [-] <value>
Translate molecule
zoom [boolean]
zoom <value>
Scale molecule
Specify magnification
slab [boolean]
slab <value>
Enable/disable slabbing
Move Z-clipping plane
centre [expression]
Set centre of rotation
reset
Initial transformation
set axes [boolean]
Display co-ordinate axes
set boundbox [boolean]
Display bounding box
set unitcell [boolean] Display crystal unit cell
set stereo [boolean]
Control L&R images
set monitor [boolean] Show distance monitor labels
set backfade [boolean]
Shade to any background color
set display selected
Currently selected portion
load [format] inline
set picking
Series of nine commands:
off | ident | distance
angle | torsion | label
monitor | center | coord
Scripted Commands
pause
echo
refresh
set write [boolean]
Load molecule
from script
Suspend script execution
Display text on
command line
Redraw image
Save & write in scripts
Atom Expressions
Export Commands
Colour Schemes
Predefined Sets:
alpha
hydrophobic
Residue Ranges:
3,16,12
9-20
Boolean Operators:
backbone and not alpha
ligand or 196-199
Primitive Expressions: cys, glu, arg, as?
ser70a, **p, glu24:1
hem*p.fe, *.sg
Comparison Operators: atomno=4,atomno=6
temperature>=900
Within Expressions:
within(8.0,ligand)
write [format] <filename> Output image file
gif
CompuServe GIF format
iris
IRIS RGB
ps, epsf
Encapsulated PostScript
monops
Monochrome PostScript
vectps
'Cartoon' PostScript
bmp
Microsoft Bitmap format
pict
Apple 'PICT' file
ppm
Portable Pixmap
sun, sunrle
Sun Rasterfile
CPK Atom Colours
Predefined Sets
write script <filename> Generate RasMol script
write povray <filename>
Generate POVray data
write vrml<filename> Generate VRMLdata
write molscript <filename>
Output MolScript script
write kinemage <filename>
Output Kinemage file
save <filename>
Save selected atoms
set kinemage <boolean> Set Mage file detail
set transparent<boolean>
Allow transparent GIFs
write phipsi<filename> Generate phi-psi data
write RDF<filename> Ramachandran plot data
write RPP<filename>
Ramachandran printer
plot
at
alpha
basic
charged
hetero
large
nucleic
pyrimidine
small
water
acidic
amino
bonded
cyclic
hydrogen
ligand
polar
selected
solvent
acyclic
aliphatic
aromatic
backbone
buried
cg
cystine
helix
hydrophobic ions
medium
neutral
protein
purine
sheet
sidechain
surface
turn
define <identifier> <expression>
User-defined sets
Rendering Commands
background <colour>
Set background colour
set ambient [value]
Depth-cueing/lighting
set shadows [boolean]
Enable/disable shadows
set specular [boolean]
set specpower [value]
Enable atom highlights
Control atom 'shininess'
set vectps <boolean>
Enable cartoon outlines
Misc. Commands
structure
connect [boolean]
renumber
DSSP secondry structure
Recalculate connectivity
Sequentially number chains
show information
show phipsi
show RPP
show sequence
show symmetry
Display molecule statistics
Display trosion angles
Ramachandran printer plot
Display molecule sequence
Display crystal space group
set mouse rasmol
set mouse quanta
set mouse insight
Default mouse bindings
Polygen's Quanta bindings
Biosym's Insight II bindings
set cisangle
CIS angle cutoff
Command Line Editing
In addition to the cursor keys, the following 'emacs'
control keys may be used to edit the command line.
Ctrl-H / Ctrl-D
Ctrl-B / Ctrl-F
Ctrl-A / Ctrl-E
Ctrl-P / Ctrl-N
Delete previous/next character
Move backward/forward a character
Move to beginning/end of line
Display previous/next history
Carbon
Oxygen
Nitrogen
Hydrogen
Sulphur
Phosphorous
Chlorine
Bromine, Zinc
Calcium
Unknown
light grey
red
sky blue
white
yellow
orange
green
brown
dark grey
deep pink
[200,200,200]
[240,0,0]
[143,143,255]
[255,255,255]
[255,200,50]
[255,165,0]
[0,255,0]
[165,42,42]
[128,128,144]
[255,20,147]
Amino Acid Colours
ASP, GLU
CYS, MET
LYS, ARG
SER, THR
PHE, TYR
ASN, GLN
GLY
LEU, VAL, ILE
ALA
TRP
HIS
PRO
others
bright red
yellow
blue
orange
mid blue
cyan
light grey
green
dark grey
pink
pale blue
flesh
tan
[230,10,10]
[230,230,0]
[20,90,255]
[250,150,0]
[50,50,170]
[0,220,220]
[235,235,235]
[15,130,15]
[200,200,200]
[180,90,180]
[130,130,210]
[220,150,130]
[190,160,110]
Secondary Structure Colours
Alpha Helix
Beta Sheet
Turns
Other
magenta
yellow
pale blue
white
[240,0,128]
[255,255,0]
[96,128,255]
[255,255,255]
Hydrogen Bond Type Colours
Offset +2
Offset +3
Offset +4
Offset +5
Offset -3
Offset -4
default
white
magenta
red
orange
cyan
green
yellow
[255,255,255]
[255,0,255]
[255,0,0]
[255,165,0]
[0,255,255]
[0,255,0]
[255,255,0]