<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 Matthias,<div class=""><br class=""></div><div class=""> I added an "interfaces select" command to select the contacting residues using buried areas to judge contacts, for example,</div><div class=""><br class=""></div><div class="">open 7mjs</div><div class="">interfaces select /X contacting /H</div><div class="">interfaces select /X contacting /H both true</div><div class=""><div>close</div><div><br class=""></div><div>open 1a3n</div><div>inter sel /A,B contacting /C,D</div><div><br class=""></div><div>More details here</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5232" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5232</a></div><div><br class=""></div><div>It will be in tonight's daily build.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><blockquote type="cite" class=""><div class="">On Sep 15, 2021, at 8:44 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Matthias,<br class="">The "interfaces" command uses a multistep procedure of calculating buried SASA between each pair of chains and then using an area cutoff to identify which residues are involved in each interface. <br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#interface-residues" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#interface-residues</a>><br class=""><br class="">You could do it with a series of "measure buriedarea" commands, one for each pairwise combination of chains. You would want to use the options to select residues with buried area greater than some cutoff value.<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea</a>><br class=""><br class="">An alternative approach is to use "contacts" instead of "measure buriedarea" for each pairwise combination of chains. Instead of buried area, this goes by distance between the VDW surfaces of the atoms ("overlap" is 0 where VDW surfaces would exactly touch, -1.0 where they are 1A apart, +1.0 where they would intersect by 1A). The reason we use overlap instead of merely distance is that it accounts for different sizes of different atoms. However it also has an option to ignore sizes and use center-center distance if that's what you want.<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html</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 Sep 15, 2021, at 6:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Dear ChimeraX team, <br class=""><br class="">I am trying to selected interface residues using the “interface” tool. While doing this through the context menu of the interface plot works, I am analyzing a larger number of PDBs and am therefore looking for a way to achieve this through the command line (the contacting chains are displayed already in the log window. Essentially I wonder if it is possible to expand this to the contacting residues).<br class=""><br class="">Thanks a lot in advcance,<br class="">Matthias<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>