<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="">I meant to also say that we have a ticket open in our bug-tracking database to make the handling of that blank column more flexible, and I will add you to the cc list for that ticket so that you’ll know when it gets worked on.<div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 15, 2020, at 10:11 AM, 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 Jacob,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I can’t answer your first question (Greg Couch, our “mmCIF guy”, is the expert there), but I can help with the second. In the PDB standard there are 3 columns allocated to the residue name, followed by a blank column and then one column for the chain ID. Some programs steal that blank column for a 4-character residue name (Amber) and some steal it for a 2-character chain ID. ChimeraX’s PDB code is based on code from Chimera, and Chimera interfaced extensively with Amber programs and therefore interprets that column as as the 4th character of the residue name. So, when that file is read in you get single-character chain IDs (which is fine in your case since you only had ~10 chains that only differed in the second character) and residue names like SERL and ALAL. Obviously, those names are non-standard and therefore ChimeraX writes them out in HETATM records.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The good news is that your problem is pretty easy to fix, at least in this particular case: just throw away the fourth character of the residue name. I have attached a simple Python script that does just that, which you just use the ‘open’ command to run (<i class="">i.e.</i> “open res-fix.py”).</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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 class=""><br class=""></div><div class=""></div></div></div><span id="cid:3E4178FF-C9E6-4BA8-84DE-155557384FA8@cgl.ucsf.edu"><res-fix.py></span><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=""><div class=""><div class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jun 13, 2020, at 2:59 PM, Anderson, Jacob <<a href="mailto:jacob_r_anderson@hms.harvard.edu" class="">jacob_r_anderson@hms.harvard.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">As an addendum, in coot, I saved OK mmcif file as a PDB (in zip as coot-mmcifTOpdb.pdb). Reviewing the file, it looks OK. It also opens and docks OK in ChimeraX with proper connectivity. However, upon saving the pdb with its updated coordinates after using the "Fit To Map" module, all the atoms have been changed to HETATM (in zip as it_to_map_PDB_savedinchimerax.pdb)</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Might this be a bug? or possibly a product of saving a cif file in coot to pdb? It was reproduced upon a second try.</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Maybe to consolidate the problems:</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">1) mmcif not connected in chimerax, but OK in coot</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">[upon trying a workaround with an OK PDB file]</div><div style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">2) A fit to map PDB, when saved with chimerax, has all atoms changed to HETATM</div><div 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=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" class=""><div class=""><div class=""></div><div id="divtagdefaultwrapper" dir="ltr" style="" class=""><p style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""></p><div style="margin: 0px; text-align: start; background-color: rgb(255, 255, 255);" class=""><font face="Arial, sans-serif" class=""><span style="font-size: 12px;" class=""><b class="">~jacob</b></span></font></div><p style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-size: 10pt; font-family: Arial, Helvetica, sans-serif;" class=""></span></p></div></div></div></div><div id="appendonsend" 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=""></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Anderson, Jacob<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Saturday, June 13, 2020 1:48 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>ChimeraX: mmcif connectivity lost in some chains; OK in Coot<span class="Apple-converted-space"> </span></font><div class=""> </div></div><div dir="ltr" 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=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Dear ChimeraX team,</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Thank you very much for your work on this great software. We use it daily, and without which it would be extremely difficult to articulate our science. </div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">I am touching base with a problem I am having after migrating from a pdb --> mmcif format.<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">For context, I am running ChimeraX on Ubuntu 20.04 using a fresh deb install this morning:</span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><span class=""> chimerax --version<br class=""></span><div class="">UCSF ChimeraX version: 1.0 (2020-06-04)<br class=""></div><div class="">© 2016-2020 Regents of the University of California. All rights reserved.<br class=""></div><span class=""></span><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">To be explicit, my problem is entirely reproducible. Specifically, I have a file (attached) that when opened in ccpem's Coot v0.9-pre, has all the connectivity present. However, when I switch to ChimeraX, the connectivity of some chains are lost. A good example of this contrast on chain connectivity fidelity is chain LA and LB. (photo attached).</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">I tried reading through the<span class="Apple-converted-space"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guidelines.html" title="https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guidelines.html" class="">ChimeraX documentation on this CIF format,</a> but it remained not totally clear to me what is going awry in some chains but not in others.</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">If you might have any insight on how to overcome this problem in chimerax, and allow all the chains to remain their connectivity, I would very much appreciate your thoughts/wisdom on the topic.</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">~Jacob</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><span id="cid:0f6782e1-eb79-43db-93e8-0f8f44417fb3" class=""><image.png></span><br class=""></div><div class=""><div id="x_Signature" class=""><div class=""><div id="x_divtagdefaultwrapper" dir="ltr" style="" class=""><p style="margin-top: 0px; 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