multiple resolution/rFree/rWork values

[wojdyr]

Hi, I'm working on a project in the same domain - reading and writing macromolecular structures, and I was just checking how you handle models with multiple refinement statistics.
For example 5moo - joint x-ray and neutron refinement.
I suppose MMTF just stores one of the values?

[pwrose]

Yes, there will be only a single value for resolution, rfree, and rwork. These are the same values as reported on the RCSB PDB structure summary page: http://www.rcsb.org/pdb/explore/explore.do?structureId=5MMO To create the MMTF files we use BioJava's mmCIF reader ( https://github.com/biojava/biojava/blob/master/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java ) and then export the data as .mmtf files. Looking at 5MMO, it reads the following mmCIF records: _refine.ls_d_res_high 1.81 _refine.ls_R_factor_R_work 0.18178 _refine.ls_R_factor_R_free 0.23884

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On Mon, Jun 19, 2017 at 6:54 AM, Marcin Wojdyr ***@***.***> wrote: Hi, I'm working on a project <https://github.com/project-gemmi/gemmi/> in the same domain - reading and writing macromolecular structures, and I was just checking how you handle models with multiple refinement statistics. For example 5moo - joint x-ray and neutron refinement. I suppose MMTF just stores one of the values? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#29>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADuwEL0QosnEZoaMU9D8q9rVK6aGuhN_ks5sFn2mgaJpZM4N-Q2H> .

-- Peter Rose, Ph.D. Director, Structural Bioinformatics Laboratory San Diego Supercomputer Center UC San Diego +1-858-822-5497

[wojdyr]

5MOO

The structure summary is missing resolution:
http://www.rcsb.org/pdb/explore/explore.do?structureId=5MOO

[josemduarte]

Biojava (SimpleMMcifConsumer class linked by @pwrose above) will use the last value encountered and that's the one written to mmtf. This is the relevant output of last mmtf files creation log:

18:30:22 [main] INFO  org.rcsb.mmtf.update.BuildMmtfFiles - Processing /mnt/ftp1/pub/pdb/data/structures/divided/mmCIF/mo/5moo.cif.gz
18:30:22 [main] WARN  org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer - More than 1 resolution value present, will use last one 1.43 and discard previous 1.44 
18:30:22 [main] WARN  org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer - More than 1 Rfree value present, will use last one 0.1848 and discard previous 0.16 
18:30:22 [main] WARN  org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer - More than 1 R work value present, will use last one 0.1700 and discard previous 0.13 

[wojdyr]

OK, thanks!