[Chimera-users] Use of sym command

Lee A.G. A.G.Lee at soton.ac.uk
Tue Jul 10 05:08:02 PDT 2018

Hi Elaine
Very many thanks for clearing that up for me!
I was hoping that there was something in Chimera like the symexp command in PyMol  that takes a protein and then creates all its crystallographic neighbours (all symmetry related objects) within  a given cut-off distance from the original molecule. I think that what I will have to do is to generate the symmetry-related molecules using PyMol, save them as PDB files, and then open them in Chimera for further handling.
Many thanks once again

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: 09 July 2018 18:17
To: Lee A.G.
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Use of sym command

Hi Anthony,
You must be referring to this message:

The PDB ID in that message contains “1”  number one not “l” letter ell.  So if you use 2o1i which is a DNA, your command will work.   It does not do anything with 2oli because that protein monomer is already the biological assembly, at least according to its page at RCSB: <https://www.rcsb.org/structure/2oli>

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

> On Jul 9, 2018, at 5:03 AM, Lee A.G. <A.G.Lee at soton.ac.uk> wrote:
> Hi Elaine
> I am trying to use the sym command to generate BIOMT-described copies of a protein. As a test I have used 2oli, as in your contribution of 12 Jan 2009. Having loaded 2oli and entered the command
> sym #0 #0
> I get the error message "No symmetric molecule copies".
> Any help gratefully received
> Anthony Lee

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