<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Greg,<div><br></div><div> I discovered that at least one of the old mmCIF example files 1voq_1vor_…1vp0.cif from the RCSB has numbers such as coordinates right justified instead of left justified as in the mmCIF files you download from the normal PDB entry pages.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://mmcif.wwpdb.org/docs/large-pdbx-examples/">http://mmcif.wwpdb.org/docs/large-pdbx-examples/</a></div><div><br></div><div>With right-justified numbers and left-justified character fields (e.g. atom name) code to guess the fixed field positions assuming every field is left-justified fails. I don’t see any way to remedy this. But I also suspect these files are obsolete.</div><div><br></div><div> Another RCSB location with 9 large mmCIF files is </div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF">ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF</a></div><div><br></div><div> Cathy Lawson suggested in the email below about 2 months ago that all split PDB entries were going to get single-file mmCIF versions within a month. I believe there are hundreds of split entries. They were supposed to appear in the above ftp directory. Apparently they only put a few there.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div><blockquote type="cite">On Mar 6, 2014, at 10:23 AM, Cathy Lawson <<a href="mailto:cathy.lawson@rutgers.edu">cathy.lawson@rutgers.edu</a><br><<a href="mailto:cathy.lawson@rutgers.edu">mailto:cathy.lawson@rutgers.edu</a>>> wrote:<br><br><blockquote type="cite">Dear Tom and Tom,<br><br>I was asked to write to both of you as a follow up to a discussion at<br>our RCSB PDB group meeting yesterday.<br>This is regarding combining of large entry split-entries into single<br>entry mmCIF files, and the ability of UCSF Chimera to handle these files.<br><br>As you are likely aware, wwPDB publicly announced last year that<br>split entries would be combined, and this work is now in progress.<br><a href="http://www.wwpdb.org/news/news_2013.html#22-May-2013">http://www.wwpdb.org/news/news_2013.html#22-May-2013</a><br><br>When the combined files are ready for release (we think this will be<br>in the next month or so),<br>they will be added to "large_structure" subdirectory of the wwPDB<br>ftp (<a href="ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/">ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/</a>)<br>for a grace-period of about six months, after which all split entries<br>will be obsoleted and large entry cifs will<br>moved into the main archive.<br><br>We are concerned about the impact that these archive changes may have<br>on the ability of UCSF Chimera to handle<br>large coordinate file entries. In my experience as well as others in<br>our group, the 3j3q mmCIF file (complete hiv capsid) in particular is<br>problematic<br>to upload/view using Chimera, either crashing or taking many hours to<br>load. Our current workaround so we can make<br>pictures is to load a PDB file containing only C-alpha atoms, but<br>even this is an extremely slow load (say 5-10 minutes, depending on<br>the machine).<br><br>We wonder whether it might be possible to develop a means to more<br>quickly load and view large structures in Chimera, <br>e.g., perhaps skipping ribbon calculations and going directly to a<br>multiscale model surface view?<br>A shortcut like this would be most welcome by to all of us who<br>regularly need to view large structures, <br>and would be similar in spirit to the way Chimera initially displays<br>large maps with binning.<br><br>Can you let me know whether there are plans along this line and if so<br>when they might be implemented in future releases?<br>Also if there is any way that we can help? (e.g., several of us would<br>be keenly interested beta-testers!)<br><br>Cheers and Best wishes,<br><br><br>Cathy<br><br><br><br>******************<br>Catherine Lawson, Ph.D.<br>EM project manager for RCSB-PDB<br><a href="http://emdatabank.org">http://emdatabank.org</a> <<a href="http://emdatabank.org/">http://emdatabank.org/</a>><br><a href="mailto:cathy.lawson@rutgers.edu">cathy.lawson@rutgers.edu</a> <<a href="mailto:cathy.lawson@rutgers.edu">mailto:cathy.lawson@rutgers.edu</a>><br>USA +1 (848) 445 5494 <br>*****************</blockquote></blockquote></div><div><br></div><div><br><div><div>On May 27, 2014, at 4:26 PM, Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello, I'm working on improving Chimera's mmCIF support. So if anyone has a mmCIF file that is not from the PDB and that they are willing to share, please send it to me.<br><br> Many thanks,<br><br> Greg<br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br><br></blockquote></div><br></div></body></html>