[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.

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.

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 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

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