Common commands in three molecular visualization programs

action

Rasmol

Chimera

Pymol

simplified display for overview

Display->Cartoon

Colours->Chain

Actions->Ribbons->Show

Actions->Atoms/Bonds->Hide

Tools->Depiction->Rainbow->Chain

all->H->Hide everything

all->S->Show cartoon

all->C->Color by chain->by chain(e. c)

identify an atom in the display

click on atom

e.g:Atom: CD2 1633 Group: HIS 77 Chain: B Model: 1

hover the cursor over the atom

e.g:#0.1 LYS 66.B CG

ctrl-click to select (ctrl-click backgrnd to deselect)

click selects residue and prints:

/file/model/group/chain/residue/atom

e.g.: /2dn1//B/HIS`92/NE2

zoom in

shift-click

right-click

right-click

adjust clipping planes

ctrl-leftclick

Favorites->Side View

shift-rightclick

select key residues

RasMol> select his87

command> select #0:87.A

PyMol> select His87, HIS`87/

display heme as sticks

RasMol> select HEM

Display->Sticks

Select->Residue->HEM

Actions->Atoms/Bonds->Show

Actions->Atoms/Bonds->Stick

PyMol> select hemes, resn HEM

(hemes)->S->Show sticks

(hemes)->C->Show sticks

export nice picture

N/A

Tools->Viewing->Effects->Subdivision Qual.>5

File->Save Image->Save As

viewport 2000,1500 increases resolution

ray creates ray-traced image

png saves it as .png file

define a group to work with

RasMol> define keyHis, his87

Select->Name Selection

PyMol> select His87, resn his

structural alignment

N/A

Tools->Structure Comaparison->MatchMaker

PyMol> align prot1////ca,prot2

calculate missing secondary structure

RasMol> structure

command> ksdssp selection

PyMol> dss selection

display electrostatic surface

N/A

calculate using GRASP (another program)

Tools->Surface/Binding Analysis->Electrostatic Surface Coloring

(1ubi)->A(ctions)->generate->vacuum electrostatics->protein contact potential (local)

[or Plugin->APBS tools]

example script

pdb_compare.rasmol

pymol_complex_compare.pml

pymol_complex.pml

online user manual

http://www.umass.edu/microbio/rasmol/distrib/rasman.htm

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html

http://pymol.sourceforge.net/newman/user/toc.html