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 |