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Rasmol Quick Reference: Atom Expressions Display Commands

The document describes commands and functions for the molecular visualization program RasMol. It provides details on commands for selecting atoms, rendering bonds and surfaces, coloring representations, and exporting images. It also lists predefined atom sets and amino acid colors.

Uploaded by

Karthi Shanmugam
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87 views2 pages

Rasmol Quick Reference: Atom Expressions Display Commands

The document describes commands and functions for the molecular visualization program RasMol. It provides details on commands for selecting atoms, rendering bonds and surfaces, coloring representations, and exporting images. It also lists predefined atom sets and amino acid colors.

Uploaded by

Karthi Shanmugam
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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RasMol

Quick Reference

Atom Expressions

Display Commands

Predefined Sets:

thickness values are in 1/250 units

alpha
hydrophobic
Residue Ranges:
3,16,12
Mouse Buttons (PC)
9-20
Boolean
Operators:
backbone and not alpha
Clicking on an atom identifies that atom in the command
ligand or 196-199
window.
not (hydrogen or hetero)
Left Button
Rotate X-Y
not *.FE and hetero
Right Button
Translate X-Y
Primitive Expressions: cys, glu, arg, as?
ser70a, **p, glu24:1
Shift Left Button
Zoom
hem*p.fe, *.sg
Shift Right Button
Rotate Z
Comparison Operators: atomno=4,atomno=6
Control Left Button
Z-Clipping (Slab)
temperature>=900
Within Expressions:
within(8.0,ligand)
(c) Copyright 1994 Roger Sayle, Updates B. Steipe

General Commands
load [format] <filename>
Load a molecule
pdb
Brookhaven Protein Databank
others
see documentation

Predefined Sets

at
acidic
acyclic
aliphatic
alpha
amino
aromatic
backbone
basic
bonded
buried
cg
zap
Delete molecule
charged
cyclic
cystine
helix
exit
Exit from RasMol
hetero
hydrogen hydrophobic ions
ligand
medium
neutral
help [topic [subtopic]]
Display on-line help large
nucleic
polar
protein
purine
topic
pyrimidine selected
sheet
sidechain
small
solvent
surface
turn
Selection
water
select <expression>
Update part of molecule
restrict <expression> Display only part of mol.
define <identifier> <expression>
User-defined
sets
*
All atoms
cys
Atoms in cysteines
Rendering Commands
hoh
Atoms in water molecules
as?
Atoms in asparagine or aspartic acid
background <colour> Set background colour
*120
Atoms at residue 120 of all chains
set ambient [value]
Depth-cueing/lighting
*p
Atoms in chain P
set
shadows
[boolean]
Enable/disable shadows
*.n?
Nitrogen atoms
set
specular
[boolean]
Enable atom highlights
cys.sg Sulphur atoms in cysteine residues
set
specpower
[value]
Control atom 'shininess'
ser70.c? Carbon atoms in serine-70
hem*p.fe Iron atoms in the Heme of chain P
*.*;A Atoms in alternate conformation A
*/4
All atoms in model 4

wireframe [boolean]
wireframe <value>

Display wireframe
Display stick bonds

spacefill [boolean]
Display spacefill spheres
spacefill <value>
Specify atom sphere radius
spacefill temperature
backbone [boolean]
backbone <value>

Display alpha backbone


Specify backbone radius

ribbons [boolean]
ribbons <value>

Display solid ribbons


Specify ribbon width

cartoon [boolean]
cartoon <value>

Display ribbon & direction


Specify width

label [boolean]
Draw default atom labels
label <string>
Label with arbitrary text
set fontsize <value> Set label font height
ssbonds [boolean]
ssbonds <value>

Display disulphide bonds


Specify ssbond radius

set ssbonds backbone SSBonds between alphas


set ssbonds sidechain SSBonds between sulphurs
hbonds [boolean]
hbonds <value>

Display hydrogen bonds


Specify hbond radius

set hbonds backbone HBonds between alphas


set hbonds sidechain HBonds donor/acceptor
monitor <#>, <#>

Draw bond and distance


between arbitrary atoms
monitor [boolean]
Turn monitor on and off
set monitor [boolean] Turn monitor label on/off
dots [boolean]
dots <value>

Display dot surface


Specify dot density

set solvent [boolean] VDW or solvent surface


set radius <value>
Specify probe sphere rad.

Amino Acid Colours

Colour Commands
colour [object] <colour>
Objects:
atoms
ribbons
ssbonds
ribbons1
Predefined
blue
greenblu
e
red
yellow

bonds
labels
dots
ribbons2

Colours:
black
magenta

Colour representation
backbone
hbonds
axes

cyan
orange

green
purple

ASP, GLU
CYS, MET
LYS, ARG
SER, THR
PHE, TYR
ASN, GLN
GLY
LEU, VAL, ILE
ALA
TRP
HIS
PRO

bright red
yellow
blue
orange
mid blue
cyan
light grey
green
dark grey
pink
pale blue
flesh

[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]

Secondary Structure Colours


redorange violet

Atom Colour Schemes:


cpk
amino
group
chain
temperature
charge
colour hbonds type
colour dots potential

white

shapely
structure
user
Colour hbonds by offset
Display potential surface

Colour Schemes

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]

CPK Atom Colours


Carbon
Oxygen
Nitrogen
Hydrogen
Sulphur
Phosphorous
Chlorine
Ca, Metals
Unknown

light grey
red
light blue
white
yellow
orange
green
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]
[128,128,144]
[255,20,147]

Export Commands
write [format] <filename>
Output image file
gif
CompuServe GIF format
ps, epsf
Encapsulated PostScript
monops
Monochrome PostScript
vectps
'Cartoon' PostScript
bmp
Microsoft Bitmap format
pict
Apple 'PICT' file
ppm
Portable Pixmap
sun,
Sun Rasterfile
sunrle
set vectps <boolean>

Enable cartoon outlines

write script <filename> Generate RasMol script


write molscript <filename> Output
MolScript
script
write kinemage <filename> Output Kinemage file
set kinemage <boolean> Set Mage file detail

Misc. Commands
structure
connect [boolean]
renumber

DSSP secondary structure


Recalculate connectivity
Sequentially number chains

show information
show sequence
show symmetry

Display molecule statistics


Display molecule sequence
Display crystal space group

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

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-DDelete previous/next character
Ctrl-B / Ctrl-F Move backward/forward a character
Ctrl-A / Ctrl-E Move to beginning/end of line
Ctrl-P / Ctrl-N Display previous/next history

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