[Chimera-users] Rotate chains independently

Elaine Meng meng at cgl.ucsf.edu
Mon May 10 08:55:15 PDT 2021

Hi Roy,
You can use the "center" option of the "turn" command to give a center of rotation.  However, to move chains separately you would need them in separate models, and also use the "models" option of the command to say which model to move.  Command usage and options shown here:

To get chains in separate models you can either
(1) open the structure multiple times.  For example if it has chains A and B that you want to move separately, open one copy and delete B so that model #0 contains only chain A.  Then open another copy of the same structure and delete chain B so that model #1 contains only chain B.
- or -
(2) use "split" command which would put the different chains in different models #0.1, #0.2, ... as you can see if you open the Model Panel from the Favorites menu.  Command usage and options shown here:

Then, for example, to move model #0.2 using a center of rotation specified as atoms:

turn z -15 models #0.2 center @ca,cb

Make sure that @ca,cb makes sense.  There might be a lot of CA and CB atoms in everything you have open, do you really mean to use the center of that whole set?  Or did you mean CA and CB in a specific residue, e.g. CA and CB in residue 12 of chain A which would be specified as

:12.A at ca,cb

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

> On May 9, 2021, at 4:11 PM, Roy Batty <roybatty269 at gmail.com> wrote:
> I have a pdb with a homodimeric conformation for two alpha helix transmembrane domains.
> This structure features a cross-like conformation, interacting at given residues.
> I want to rotate each of the domains 15º along the z-axis.
> So for example, something like this would be fine:
> select :.A                (select chain A)
> turn z -15 @ca,cb  (rotate chain A 15º, from the residues given as an anchor point)
> Is there anything like this? Thx

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