Hi Greg, 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. http://mmcif.wwpdb.org/docs/large-pdbx-examples/ 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. Another RCSB location with 9 large mmCIF files is ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF 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. Tom

On Mar 6, 2014, at 10:23 AM, Cathy Lawson <cathy.lawson@rutgers.edu <mailto:cathy.lawson@rutgers.edu>> wrote:

...

Dear Tom and Tom,

I was asked to write to both of you as a follow up to a discussion at our RCSB PDB group meeting yesterday. This is regarding combining of large entry split-entries into single entry mmCIF files, and the ability of UCSF Chimera to handle these files.

As you are likely aware, wwPDB publicly announced last year that split entries would be combined, and this work is now in progress. http://www.wwpdb.org/news/news_2013.html#22-May-2013

When the combined files are ready for release (we think this will be in the next month or so), they will be added to "large_structure" subdirectory of the wwPDB ftp (ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/) for a grace-period of about six months, after which all split entries will be obsoleted and large entry cifs will moved into the main archive.

We are concerned about the impact that these archive changes may have on the ability of UCSF Chimera to handle large coordinate file entries. In my experience as well as others in our group, the 3j3q mmCIF file (complete hiv capsid) in particular is problematic to upload/view using Chimera, either crashing or taking many hours to load. Our current workaround so we can make pictures is to load a PDB file containing only C-alpha atoms, but even this is an extremely slow load (say 5-10 minutes, depending on the machine).

We wonder whether it might be possible to develop a means to more quickly load and view large structures in Chimera, e.g., perhaps skipping ribbon calculations and going directly to a multiscale model surface view? A shortcut like this would be most welcome by to all of us who regularly need to view large structures, and would be similar in spirit to the way Chimera initially displays large maps with binning.

Can you let me know whether there are plans along this line and if so when they might be implemented in future releases? Also if there is any way that we can help? (e.g., several of us would be keenly interested beta-testers!)

Cheers and Best wishes,

Cathy

****************** Catherine Lawson, Ph.D. EM project manager for RCSB-PDB http://emdatabank.org <http://emdatabank.org/> cathy.lawson@rutgers.edu <mailto:cathy.lawson@rutgers.edu> USA +1 (848) 445 5494 *****************

On May 27, 2014, at 4:26 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:

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.

Many thanks,

Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users