Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities
This looks like the mapping you are after: http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html It maps only the structured PDB data items to their equivalent mmCIF items. For instance REMARK 2 is not there, but REMARK 200 is. The resolution value should then be in REMARK 200 RESOLUTION RANGE HIGH (corresponding to mmCIF data item _refine.ls_d_res_high). Jose On 07.07.2015 19:05, Phil Jeffrey wrote: I'm updating some code to have limited mmCIF/PDB format interoperability and have hit a snag. While I can infer the connection between some data items in the PDB header REMARK and the items in mmCIF I can't definitively deduce some others. In particular the mapping of REMARK 2 RESOLUTION seems a little ambiguous and the dictionary documentation doesn't help in this regard. Does anyone know where to find an explicit mapping of one data field to another between the two formats ? (I don't expect there to be a data field in the PDB header for everything in mmCIF but I do for the reverse case). Thanks Phil Jeffrey Princeton
Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities
REMARK 2 is generated from _refine.ls_d_res_high http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html Regards John On Wednesday 08 July 2015 15:04:45 Jose Manuel Duarte wrote: This looks like the mapping you are after: http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html It maps only the structured PDB data items to their equivalent mmCIF items. For instance REMARK 2 is not there, but REMARK 200 is. The resolution value should then be in REMARK 200 RESOLUTION RANGE HIGH (corresponding to mmCIF data item _refine.ls_d_res_high). Jose On 07.07.2015 19:05, Phil Jeffrey wrote: I'm updating some code to have limited mmCIF/PDB format interoperability and have hit a snag. While I can infer the connection between some data items in the PDB header REMARK and the items in mmCIF I can't definitively deduce some others. In particular the mapping of REMARK 2 RESOLUTION seems a little ambiguous and the dictionary documentation doesn't help in this regard. Does anyone know where to find an explicit mapping of one data field to another between the two formats ? (I don't expect there to be a data field in the PDB header for everything in mmCIF but I do for the reverse case). Thanks Phil Jeffrey Princeton -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529
Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities
Thanks Jose - I missed that one. REMARK 2 is somewhat ambiguous with: _refine.ls_d_res_high and _reflns.d_resolution_high although the former makes more sense and seems to be what corresponds to REMARK 2. Haven't yet seen an entry with only _reflns.d_resolution_high and not _refine.ls_d_res_high but there are several where the resolution of refinement is apparently significantly higher than the resolution of the source data: 1AU7, 1AW7 etc. Cheers Phil Jeffrey Princeton On 7/8/15 10:04 AM, Jose Manuel Duarte wrote: This looks like the mapping you are after: http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html It maps only the structured PDB data items to their equivalent mmCIF items. For instance REMARK 2 is not there, but REMARK 200 is. The resolution value should then be in REMARK 200 RESOLUTION RANGE HIGH (corresponding to mmCIF data item _refine.ls_d_res_high). Jose
Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities
On Tuesday, 07 July, 2015 13:05:55 Phil Jeffrey wrote: I'm updating some code to have limited mmCIF/PDB format interoperability and have hit a snag. While I can infer the connection between some data items in the PDB header REMARK and the items in mmCIF I can't definitively deduce some others. In particular the mapping of REMARK 2 RESOLUTION seems a little ambiguous and the dictionary documentation doesn't help in this regard. So far as I know, anything that begins with REMARK is not guaranteed to follow any standardized convention. Different programs fill in different things here, and depositors can add new stuff. The current PDB documentation states: REMARK 2 states the highest resolution, in Angstroms, that was used in building the model. As with all the remarks, the first REMARK 2 record is empty and is used as a spacer. Used in building the model is nicely ambiguous, so I doubt that you can map it uniquely to any single value reported by some particular program. Ethan Does anyone know where to find an explicit mapping of one data field to another between the two formats ? (I don't expect there to be a data field in the PDB header for everything in mmCIF but I do for the reverse case). Thanks Phil Jeffrey Princeton -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
