[Chimera-users] Grouping Molecules

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 23 13:29:51 PDT 2010

Hi Rocco,
If you are just going to be moving the molecules with commands (turn, roll, etc.), you can specify in the command exactly which models should move and what to use as the center of rotation.

However, if you mean interactive rotation with the mouse, here are some possibilities:

(1) merge A & B into one model, C & D into another model.  This could be done with the combine command or the copy/combine function in the Model Panel.  However, to avoid residue-specifier conflicts, it will change chain IDs or residue numbering as needed.

(2) try opening A and B with the same model number, even though they are still separate models, and do the same for C and D.  This could be done with the open command, e.g.

open 0 /location/location/A.pdb
open 0 /location/location/B.pdb

This will not change chain IDs or residue numbers, but conversely, there may be difficulty in independently specifying residues (for example, #0:3.A could then specify two residues, one from each model, and there would be no way to specify them individually from the command line).

Then, after 1) or 2) above, you could use the "independent" rotation mode, set in the Rotation tool or using the command: set independent

Yet another caveat is that in this independent mode, you can't control exactly what the centers are, only that different model numbers use different ones.

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

On Jun 23, 2010, at 12:26 PM, Varela, Lawrence Rocco wrote:

> Is there a way of grouping molecules in Chimera?  Here is my situation.  I have 4 molecules A, B, C, and D and I want to group A with B and C with D so that A and B has one center of rotation and C and D has another center of rotation.
> Rocco

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