<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=""><div class=""></div><div><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; 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; display: inline-block; width: 492.9375px;" 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=""></span><div id="divRplyFwdMsg" 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=""><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"><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; 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><span id="cid:E2312170-76A5-4C93-A44A-200D3A6A3F81@cgl.ucsf.edu"><pdb_hetatm_files.zip></span><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; 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