<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=""><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 10, 2018, at 12:26 AM, Fabian Glaser <<a href="mailto:fabian.glaser@gmail.com" class="">fabian.glaser@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Eric,<div class=""><br class=""></div><div class="">Thanks for your detail answer, so maybe the only thing it will be really useful now is to be able to color the residues with consurf colors in ChimeraX, with that I will be able to make figures for a paper, which is what I am after at this point. </div><div class=""><br class=""></div><div class="">Of course we would be very happy to get a script for ChimeraX at some point that could be included in our output pages.<br class=""><div class="">
<div dir="auto" style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class="">Best,<br class=""><br class="">Fabian<br class=""><br class=""><i class="">Fabian Glaser PhD</i><br class=""><br class=""><i class="">Head of the Structural Bioinformatics section </i><br class=""><i class="">Bioinformatics Knowledge Unit - BKU</i><br class=""><i class="">The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering</i><br class=""><i class="">Technion - Israel Institute of Technology, Haifa, Israel</i><br class=""><i class="">Web <a href="http://bku.technion.ac.il/" class="">http://bku.technion.ac.il/</a></i><br class=""><i class="">Tel +972 (0) 4 8293701</i><br class=""><br class=""></div></div></div></div></div>
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On 10 Apr 2018, at 1:59, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Fabian,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>ChimeraX is not backwards compatible with Chimera, so a Chimera session file cannot be opened in ChimeraX — such as what you tried to do below. We want to add a tool to <i class="">Chimera</i> that will write out a file that ChimeraX can read to restore the Chimera session as best it can, but we haven’t gotten there yet.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Furthermore, although ChimeraX can display sequence alignments, its capabilities in that regard are currently much less than what Chimera offers. The features it lacks that ConSurf uses are:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>1) Read Clustal ALN alignments</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>2) Show alignment headers</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>2b) Make header values available as residue attributes</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>3) Show Phylogeny trees</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>4) Color alignment/structures from coloring file</div><div class=""><br class=""></div><div class="">To show ConSurf results in even bare bones form would require #1 and #4, and obviously #2 and #3 add a lot of value. So I’d say ChimeraX is not “ConSurf ready” yet. What I will do is open an “enhancement request” ticket in our bug database with you on the recipient list. As the above features get added I will update the ticket and at whatever point you feel it’s worthwhile you could work on getting ConSurf to deliver ChimeraX results. I would help with any questions or issues that popped up. Sorry I don’t have better news.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div></div>
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 8, 2018, at 7:56 AM, Fabian Glaser <<a href="mailto:fabian.glaser@gmail.com" class="">fabian.glaser@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="font-family: ArialMT; font-size: 14px;" class="">Hi, </span><div class="" style="font-family: ArialMT; font-size: 14px;"><br class=""></div><div class="" style="font-family: ArialMT; font-size: 14px;">I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX</div><div class="" style="font-family: ArialMT; font-size: 14px;"><br class=""></div><div class=""><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;">ModuleNotFoundError: No module named 'cPickle'<br class=""><br class="">File "consurf_final_zn.py", line 1, in <br class=""><br class=""><span class="" style="font-style: italic;">See log for complete Python traceback.</span><br class=""><br class="">If you wish to report this error, send mail to <a href="mailto:chimerax-bugs@cgl.ucsf.edu" class="">chimerax-bugs@cgl.ucsf.edu</a> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created.</div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;"><br class=""></div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;">Is this something that can be fixed or updated?</div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;"><br class=""></div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;">More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that?</div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;"><br class=""></div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;">Here is the beginning of the original chimera script</div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;"><br class=""></div><div class="" style="margin: 0px;"><font face="ArialMT" class=""><span style="font-size: 14px;" class="">import cPickle, base64<br class="">try:<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>from SimpleSession.versions.v65 import beginRestore,\<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span> registerAfterModelsCB, reportRestoreError, checkVersion<br class="">except ImportError:<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>from chimera import UserError<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>raise UserError('Cannot open session that was saved in a'<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span> ' newer version of Chimera; update your version')<br class="">checkVersion([1, 12, 41623])<br class="">import chimera<br class="">from chimera import replyobj<br class="">replyobj.status('Restoring session...', \<br class=""> blankAfter=0)<br class="">replyobj.status('Beginning session restore...', \<br class=""> blankAfter=0, secondary=True)<br class="">beginRestore()<br class=""><br class="">def restoreCoreModels():<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>from SimpleSession.versions.v65 import init, restoreViewer, \<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span> restoreMolecules, restoreColors, restoreSurfaces, \<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span> restoreVRML, restorePseudoBondGroups, restoreModelAssociations<br class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>molInfo = </span></font></div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;"><br class=""></div><div class="" style="font-family: ArialMT; font-size: 14px; margin: 0px;">Thanks a lot,</div><div class="" style="font-family: ArialMT; font-size: 14px;"><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><br class="">Best,<br class=""><br class="">Fabian<br class=""><br class="">Fabian Glaser PhD<br class=""><br class="">Head of the Structural Bioinformatics section <br class="">Bioinformatics Knowledge Unit - BKU<br class="">The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering<br class="">Technion - Israel Institute of Technology, Haifa, Israel<br class="">Web <a href="http://bku.technion.ac.il/" class="">http://bku.technion.ac.il/</a><br class="">Tel +972 (0) 4 8293701</div></div></div></div>_______________________________________________<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://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></body></html>