<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="">Great! Happy I could help, and thanks for the props. :-)<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 18, 2019, at 8:27 PM, Zachariah Schuurs <<a href="mailto:zachariah.schuurs@hdr.qut.edu.au" class="">zachariah.schuurs@hdr.qut.edu.au</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Eric,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks so much for the help, it has achieved exactly what I desired. I will certainly be using this new knowledge of the API in the future. You guys have such great support.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Cheers<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><span class="Apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Saturday, 16 November 2019 5:10 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Zachariah Schuurs <<a href="mailto:zachariah.schuurs@hdr.qut.edu.au" class="">zachariah.schuurs@hdr.qut.edu.au</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> BB <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Programmatic trimming of PDB files based on alignment with reference structure<o:p class=""></o:p></span></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Hi Zachariah,<o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>So you would call match() twice, once to get the full correspondence between reference and match domains (<i class="">i.e.</i> turning iteration off so that no residues get dropped) and a second time to get the best superposition. This assumes that you actually care about the superposition and not just the correspondences. If you don’t care about the superposition, you can skip the second match().<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>So, to turn iteration off, make the same call you were making except with<span class="Apple-converted-space"> </span><i class="">iterate=None</i>. The returned value will be a list of tuples, each tuple containing 4 values: the moving atoms, the reference atoms, the RMSD for the actually matched atoms after iteration, the RMSD across all the initial atoms. Since you are matching only one chain, the list will contain only one tuple, so:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span><i class="">m = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND], iterate=None)</i><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span><i class="">match_atoms, ref_atoms, iteration_rmsd, full_rmsd = m</i><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">You could then select the residues of the matched domain with:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span><i class="">from chimera.selection import setCurrent</i><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> <span class="Apple-converted-space"> </span></i></span><i class="">setCurrent([a.residue for a in match_atoms])</i><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Then you can do whatever you want with the selected atoms/residues,<span class="Apple-converted-space"> </span><i class="">e.g.</i> save them to a PDB file with the ‘write’ command.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">—Eric<o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">On Nov 14, 2019, at 8:17 PM, Zachariah Schuurs <<a href="mailto:zachariah.schuurs@hdr.qut.edu.au" style="color: purple; text-decoration: underline;" class="">zachariah.schuurs@hdr.qut.edu.au</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Eric,</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks for the detailed reply. The script used some information from a previous question on the mailing list for MatchMaker, and therefore it uses MatchMaker.match() to match the reference file to the protein files in question. It is as follows:</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> s1, s2 = openModels.list(modelTypes=[Molecule])</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> c1, c2 = s1.sequence('A'), s2.sequence(chain)</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div></div><div style="margin-left: 36pt;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">m = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND], iterate=defaults[ITER_CUTOFF])</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> RMSD = (m[-1][-1])</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Some further guidance on accessing the matched atom objects and thereby the matched domain would be greatly appreciated. Playing around a bit with the code I see the reference atoms, corresponding atoms and the RMSD values. Would it just be a matter of accessing the corresponding matched atoms and outputting a PDB file of those? Or would it still need to be trimmed?</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks for the help!</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">pett@cgl.ucsf.edu</a>><span class="apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="apple-converted-space"> </span>Friday, 15 November 2019 11:26 AM<br class=""><b class="">To:</b><span class="apple-converted-space"> </span>Zachariah Schuurs <<a href="mailto:zachariah.schuurs@hdr.qut.edu.au" style="color: purple; text-decoration: underline;" class="">zachariah.schuurs@hdr.qut.edu.au</a>><br class=""><b class="">Cc:</b><span class="apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [Chimera-users] Programmatic trimming of PDB files based on alignment with reference structure</span><o:p class=""></o:p></div></div></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Hi Zachariah,<o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>I can see three possible approaches to extracting the information you need:<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">1) Call the underlying routine that MatchMaker uses. I’m guessing your script is doing something like<span class="apple-converted-space"> </span><i class="">runCommand(“matchmaker #0 #1”)</i> to do the matching, and that call returns nothing. The pertinent call is MatchMaker.match(…). It returns the reference atoms, corresponding matched atoms, and raw and pruned RMSDs. I’d say you’d have to be pretty Python savvy to use this approach because coming up with the arguments to the MatchMaker.match() call and processing the return values will require a good working knowledge of Python and how Chimera’s Python API works. Anyway, if you took this approach you would first call MatchMaker.match() with no iteration and the returned matched atoms would indicate the domain on the matched structure. If you decide to take this approach I could offer further guidance.<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">2) Extract the information from the Multalign Viewer tool. Probably the most practical approach, even if it is somewhat tricky. Since the Multalign Viewer tool is only available if the Chimera interface is shown, you won’t be able to run the script without the interface (<i class="">i.e.</i> with the --nogui flag). Anyway, once you run the matchmaker command to generate the MAV instance, use the<i class="">findMAV()</i> function shown in this previous chimera-users message: <a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010016.html" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010016.html</span></a> to the MAV Python instance. Assuming the domain on the reference is selected (and only that is selected), you can get a list of those residues with:<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span><i class="">from chimera.selection import currentResidues</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">ref_domain = currentResidues()</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">and assuming the MAV instance is in the variable <i class="">mav</i>, you can get a list of the corresponding matched residues with:<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span><i class="">match_domain =[]</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">ref_seq, match_seq = mav.seqs</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">ref_map = ref_seq.matchMaps.values()[0]</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">match_map = match_seq.matchMaps.values()[0]</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">for ref_r in ref_domain:</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">pos = ref_map[ref_r]</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">try:</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">match_domain.append(match_map[pos])</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">except KeyError:</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">pass</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">then you can select those residues with:<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span><i class="">from chimera.selection import setCurrent</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><i class=""> </i></span><span class="apple-converted-space"><i class=""> </i></span><i class="">setCurrent(match_domain)</i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Now the matched domain (only) should be selected and you can go on to do whatever you would do with that. You should probably also call<span class="apple-converted-space"> </span><i class="">mav.Quit()</i> to close the MAV instance.<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">3) Use ChimeraX. In ChimeraX, the<span class="apple-converted-space"> </span><i class="">chimera.runCommand(…)</i> equivalent (<i class="">chimerax.core.commands.run(…)</i>)<span class="apple-converted-space"> </span><b class="">does</b> return the match values, such as the atom correspondences, so as you can imagine things would be simpler. I don’t know if ChimeraX does everything else you intend to do or not, but it certainly does the things you mentioned. It is also faster than Chimera, and can run the script in nogui mode, if either of those are relevant. I can provide further guidance here also if you choose this route.<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">—Eric<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""><br class=""><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>Eric Pettersen</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""> </span></span><span class="apple-converted-space"><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""> </span></span><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">UCSF Computer Graphics Lab</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span><br class=""><br class=""><br class=""><o:p class=""></o:p></div></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">On Nov 13, 2019, at 7:56 PM, Zachariah Schuurs <<a href="mailto:zachariah.schuurs@hdr.qut.edu.au" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">zachariah.schuurs@hdr.qut.edu.au</span></a>> wrote:<o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear Chimera Team,</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have a reference protein domain and then a series of PDB files which all contain the same domain. I have programmatically been able to script an alignment of the reference to the same domain in the other files whereby he domain in the proteins of interest are isolated using the zone select method. This however leaves me with fragments and often misses some of the domain features of the interest proteins that occur outside of the specified zone.</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am wondering if it is possible to write a python script that selects the area on the protein of interest by selecting the residues in the sequence alignment after MatchMaker is conducted. For instance – protein #0 is my reference protein, which is 150 residues long. My protein of interest contains the same domain as the reference, but is 500 residues long. Upon conducting MatchMaker and getting an output sequence alignment, the 150 residues of #0 (the reference) are selected, along with the aligned residues in the protein of interest. It is possible to select the residues in the sequence alignment window (as in the picture) but I wish to be able to script it. The selected 150 residues (or so) in the protein of interest are then saved as their own trimmed file. I have been able to write a python script for completing the MatchMaker etc, but I am not sure how to achieve the selection of residues in #1 based of the alignment with #0, or if it is even possible.</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><b class=""><span style="font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class="">Zachariah Schuurs</span></b><b class=""><span style="font-family: Calibri, sans-serif; color: rgb(0, 112, 192);" class=""> </span></b><b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 112, 192);" class=""> </span></b><b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class="">| PhD Candidate </span></b><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><b class=""><span style="font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class="">CARP – Cancer & Ageing Research Program</span></b><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Institute of Health and Biomedical Innovation</span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class=""> <b class="">|</b> </span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Queensland University of Technology</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Level 6</span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class=""> </span><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class="">|</span></b><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class=""> </span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Translational Research Institute</span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class=""> </span><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class="">|</span></b><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class=""> </span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">37 Kent St</span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class=""> </span><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class="">|</span></b><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class=""> </span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Woolloongabba QLD 4102</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(146, 208, 80);" class="">T: </span></b><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(68, 84, 106);" class="">+61 7 3443 7296</span><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(0, 112, 192);" class=""> <b class=""> </b></span><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class="">| </span></b><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(146, 208, 80);" class="">E:</span></b><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(146, 208, 80);" class=""> </span><u class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(5, 99, 193);" class=""><a href="mailto:zachariah.schuurs@hdr.qut.edu.au" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">zachariah.schuurs@hdr.qut.edu.au</span></a></span></u><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class="">| </span></b><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(146, 208, 80);" class="">Web</span></b><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(166, 166, 166);" class="">: </span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="http://www.carp.org.au/" style="color: purple; text-decoration: underline;" class=""><b class=""><span style="font-size: 10pt; color: rgb(5, 99, 193);" class="">www.carp.org.au</span></b></a></span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><image002.jpg></span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></i><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; 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If you receive this email by mistake, please notify the sender immediately and delete the original email.</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><image004.png></span><o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">_______________________________________________<br class="">Chimera-users mailing list:<span class="apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: rgb(149, 79, 114);" class="">Chimera-users@cgl.ucsf.edu</span></a><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""><br class="">Manage subscription:<span class="apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: rgb(149, 79, 114);" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p class=""></o:p></div></div></div></blockquote></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""> <o:p class=""></o:p></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">_______________________________________________<br class="">Chimera-users mailing list:<span class="apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: purple;" class="">Chimera-users@cgl.ucsf.edu</span></a><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""><br class="">Manage subscription:<span class="apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: purple;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p class=""></o:p></div></div></blockquote></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>