[chimerax-users] Problem with C2 symmetric assemblies

[Y. Mutum]

Thanks!
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 30 November 2020 21:00
To: Y. Mutum <ym337 at cam.ac.uk>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Problem with C2 symmetric assemblies

Hi Yaikhomba,
I think you need to use

sym #1 assembly 2 copies true

Otherwise the symmetry partner will only be a graphical clone, not a true atomic copy.   As I understand it, you need full atomic copies to do various analyses and calculations on the coordinates.

That will give you #1 original 1be3, and #2.1, #2.2 1be3 symmetry partners.  If you don't want #1 then use command "close #1".

Then in commands you can specify the two copies of chain C, for example, as #2.1/C and #2.2/C.  If there was just a graphical clone, as from the sym command you used, there is no way to specify the two C chains from two copies of 1be3 separately, since one of them isn't "real."

(B) Alternatively, if you must have the dimer as a single model:  since ChimeraX does not yet have a "combine" command, you would need to open the assembly as a single model, e.g. from PDBe:

open 1be3 from pdbe_bio

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>

This will give you both assemblies #1.1 and #1.2, and you know that you only want assembly 2, so you would still need to close #1.1.  Then finally you would have assembly 2 as a single model, #1.2.  Unfortunately there is no way to get only the assembly you want if it is not the first one.

#1.2 from PDBe will have unique chains.  For example, the other copy of chain A is chain AA.

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 30, 2020, at 11:13 AM, Y. Mutum <ym337 at cam.ac.uk> wrote:
>
> Hi
>
> I have a a C2-symmetric pdb: 1be3 and have created a symmetric assembly using the command.
> >>> sym #1 assembly 2 newModel false
>
> The idea is to superimpose Chain /C of 1be3 and its symmetry partner with that of 3cx5 (corresponding chains -C and N) to get of deviations b/w the chains.
> However, when I try to 'match #1/C with #2/C, then I am getting only half of the C2 symmetric assembly superimposed. Is there a way to superimpose both of the chains-C of 1be3 to 3cx5?
>
> I could open the model 1be3 twice and then superimpose to the equivalent subunits (chains C and N) of 3cx5, one at a time. But the resulting superimposed assembly 1be3 (from 2 different models) is not going to be the C2 symmetric.
>
> In short, for 1be3: pdb, is it possible to rename the symmetry mate with different chains and get the C2 symmetric assembly as a single model? Say, for this new 1be3 C2-symetric assembly, you rename the second symmetry partners chains - Chain C as C1, Chain B as B1 for example in that new model. The idea is to have a C2 symmetric model with different chains, so that it can be compared with other models easily.
>
> Thanks
> Yaikhomba

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