[Chimera-users] mmCIF support

[Tom Goddard]

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 at rutgers.edu
> <mailto:cathy.lawson at 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 at rutgers.edu <mailto:cathy.lawson at rutgers.edu>
>> USA +1 (848) 445 5494 
>> *****************



On May 27, 2014, at 4:26 PM, Greg Couch <gregc at 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
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