[Chimera-users] Labeling 3D structures in Chimera (and saving them as such)

[Elaine Meng]

Hi Bilal,
We're happy to hear you might use Chimera in your lab!

As you have seen, the usual "atomic structure" formats (PDB, mol2, etc.) only describe the atomic positions and do not include labels, display styles, colors, etc.  However, different graphics programs including Chimera provide ways of saving all that information too.

I assume you want a 3D structure that can be manipulated by the students, as opposed to a 2D image.  (You could just use File... Save Image if you only wanted a picture.)

Possibilities in Chimera:

(1) The simplest is to save a Chimera session file, which can be done with the File menu or the command "save" -- later opening that file will restore the session. Disadvantages are that the file may be largish, and its contents are not meant for viewing in a text editor (it is Python code including all the structure and display data).  Information on sessions:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html>

(2) Create a Chimera command file that does the coloring, labeling, etc. Just opening the command file (a plain text file named *.com or *.cmd) in Chimera will execute the commands.  The command file could also open the structure.  Example command file contents:
  
open 2gbp
preset apply int 1
~disp solvent
align ligand protein
focus ligand z<3
rlabel :152,183

In that example, the structure 2gbp is fetched from the PDB, but you could also give a local file including its location.  Or, the students could be told to open the PDB file and then the command file (which in that case would not include the opening step).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

(3) Fancier packaging of such a command file.  
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command>

Namely, starting with the same Chimera commands, one could: 
(A) create a Demo in Chimera (there are a couple of examples to play back in the Tools... Demos menu)
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html>

(B) create a Chimera "Web data" file; clicking a link to such a file then calls the locally downloaded Chimera as a helper application.  Also requires minor setup by webmaster.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 6, 2011, at 9:24 AM, Bilal Asif wrote:

> Hello,
> I am a senior undergraduate student at Stony Brook University, part of a team currently attempting to design an introductory biology lab for biology undergraduates. We are attempting to use Chimera as a way to introduce students to structural biology and research. 
> 
> However, we have run into a problem, one which we hope you can help us solve. We have discovered that if one attaches a label to a molecule in Chimera, one cannot save it as a .pdb, and open it again with the same labels attached. Is there a way to preserve labels attached to 3D structures, perhaps by saving it in a different file format?
> 
> Thank you for your time and consideration. Any insight would be greatly appreciated. 
> Bilal Asif
> Stony Brook University
>