<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 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="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-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><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://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>