[Chimera-users] Use of sym command

Tom Goddard goddard at sonic.net
Wed Jul 11 13:03:50 PDT 2018

Hi Anthony,

  You can make copies of a molecule using crystal symmetry in Chimera with the crystalcontacts command:

	open 2o1i
	crystalcontacts #0 5 copies true schematic false

This makes copies within 5 Angstroms of 2o1i.

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/crystalcontacts.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/crystalcontacts.html>


> On Jul 10, 2018, at 5:08 AM, Lee A.G. <A.G.Lee at soton.ac.uk> wrote:
> 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
> Anthony
> ________________________________________
> 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:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003446.html>
> 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
> -----
> 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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