[Chimera-users] Symmetry generation question

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 29 09:28:02 PDT 2013


Hi Bala,
I believe you would need:

sym #0 group #1

… assuming the template model #1 has biological unit information (REMARK 350 BIOMT) information in its header.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

If the template instead has symmetry information in other types of symmetry records, you may need to take a slightly longer approach:
(a) show symmetry copies of the template, e.g. with the Unit Cell tool
(b) open extra copies of your modeled protein
(c ) superimpose the copies of the modeled protein onto those of the template.  Probably the matchmaker approach would be easiest.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

If the template does not have symmetry information in its header, you would need to somehow obtain a PDB file with the template already in the multimeric state (possibly hand-modeled) and then proceed with the third step above, or you could specify symmetry directly in the sym command with various keywords (group, axis, center…), but that can be difficult.

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 Oct 29, 2013, at 7:52 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:

> Hello,
> 1) I have modelled one chain of a multimer. Since this is a modelled structure I dnt have any symmetry information in my pdb. In such case, how can I generate the symmetry related copies. Say I want to apply a fivefold symmetry along z-axis, how can I achieve it ?
> 
> 2) I used a template structure from PDB to model my structure. What is the correct way to apply the symmetry of existing pdb model to my modeled chain.
> 
> I tried this as follows, I opened my model as #0 and then the template pdb structure #1 and tried the following sym command and obtained an error as '#0 has no biological unit info.'
> 
> sym #0 #1
> 
> Thanks,
> Bala




More information about the Chimera-users mailing list