[chimerax-users] Set up to take pictures of structure with a specific angle

[Elaine Meng]

Hi Emilie,
(1) Cartoon thickness. You would use the "cartoon style" command to change the ribbon dimensions and shape.  It can be done separately for helix, strand, and coil.  For example:

cartoon style coil thickness 1.0

There are many options, see:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

(2) Multiple images from different sessions with same orientation.

  (A) If all your different sessions were made with either the same starting structure (same PDB file) or structures that were already fit on each other when they were opened, you could get matrix from the view that you want and apply the matrix to all the others.  You would use "view matrix" without arguments in the session that already has the view you want, to report the camera matrix in the Log.  Then you would use "view matrix" specifying that camera matrix in your other sessions to put them into the same view.

  (B) If all your different sessions were made with different PDBs that weren't already fit on each other, then I believe the only way is to include a reference structure in each one, make sure the reference structure is in the position you want as in (A) above, and match the structure for the image onto the reference structure (e.g. with matchmaker or align), and then hide the reference structure.

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

> On Nov 24, 2020, at 12:45 AM, EMILIE MONTELLIER <emilie.montellier at univ-grenoble-alpes.fr> wrote:
> 
> Dear ChimeraX users, 
> 
> I have worked on p53 structure, and the goal was to highlight certain residues on the structure. I have about 10 files of the same p53 structure (same PDB) with different groups of residues highlighted and now I would like to take pictures of them with the same display of the protein (same angle, rotation) in order to compare the 10 pictures together on a same figure. Is there a way to copy the angle/rotation of one p53 structure, and to apply it to another p53 structure?
> 
> Also, is there a way to increase specifically the thickness of what is not alpha helix or beta sheet (the kind "spaghetti" structure)? 
> 
> Thanks by advance for your help, 
> Regards, 
> Emilie