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> Tom
On Jul 10, 2018, at 5:08 AM, Lee A.G. <A.G.Lee@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@cgl.ucsf.edu] Sent: 09 July 2018 18:17 To: Lee A.G. Cc: chimera-users@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@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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