<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Anthony,<div class=""><br class=""></div><div class=""> You can make copies of a molecule using crystal symmetry in Chimera with the crystalcontacts command:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 2o1i</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>crystalcontacts #0 5 copies true schematic false</div><div class=""><br class=""></div><div class="">This makes copies within 5 Angstroms of 2o1i.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/crystalcontacts.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/crystalcontacts.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 10, 2018, at 5:08 AM, Lee A.G. <<a href="mailto:A.G.Lee@soton.ac.uk" class="">A.G.Lee@soton.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Elaine<br class="">Very many thanks for clearing that up for me!<br class="">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.<br class="">Many thanks once again<br class="">Anthony<br class=""><br class=""><br class="">________________________________________<br class="">From: Elaine Meng [<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>]<br class="">Sent: 09 July 2018 18:17<br class="">To: Lee A.G.<br class="">Cc: <a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class="">Subject: Re: [Chimera-users] Use of sym command<br class=""><br class="">Hi Anthony,<br class="">You must be referring to this message:<br class=""><<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003446.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003446.html</a>><br class=""><br class="">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: <<a href="https://www.rcsb.org/structure/2oli" class="">https://www.rcsb.org/structure/2oli</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><blockquote type="cite" class="">On Jul 9, 2018, at 5:03 AM, Lee A.G. <<a href="mailto:A.G.Lee@soton.ac.uk" class="">A.G.Lee@soton.ac.uk</a>> wrote:<br class=""><br class="">Hi Elaine<br class="">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<br class="">sym #0 #0<br class="">I get the error message "No symmetric molecule copies".<br class="">Any help gratefully received<br class="">Anthony Lee<br class=""></blockquote>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>