[phenixbb] phenix refinement question
martainn_oshiomains at btinternet.com
Fri Nov 19 06:39:37 PST 2010
just to clear up some points raised on the treatment of TLS during PDB deposition.
It is not strictly the case that TLS is neglected during pdb deposition. The requirement for deposition now is that full ANISOU values have to be present if TLS has been used. In which case the TLS definitions are redundant as the full description of the ADP model is provided by the ATOM and ANISOU records.
There is therefore no absolute requirement for the TLS definitions in the header to be correctly read in order for the validation to proceed.
This aids accurate validation of the model against the provided SF data using EDS for example. The output with and without TLS was used historically to check whether the TLS definitions had been read correctly.
Having said that the presence of TLS definitions is still informative for users of the coordinates to check that for example a full anisotropic refinement has not been carried out.
PDB curation involves checking the description of the TLS groups that have been chosen. So, for example, it is useful that the selection expressions do not refer to ranges of residues that do not exist (for example "RESID -99:9999" for a 1-100 residue protein), or to overlapping ranges, for example: a chain with its TLS group 1 defined as "RESID 45:90" and its TLS group 2 is defined as "RESID 75:150".
Depending on the wwPDB deposition site, the validation programs may differ. PDBe uses an in-house version of the EDS server which uses REFMAC with TLS taken into account. RCSB and PDBj run the particular program that was used in determining the structure for validation, in addition to a validation check using SFCHECK.
It is worth saying that the PDB sites are not attempting to completely reproduce the authors' Rfactors but instead to check the deposition - so for example to spot if an incorrect SF file has been uploaded, or that space group definitions are inconsistent.
You can check the details of the PHENIX header format for TLS at
wwPDB at EBI
Protein Data Bank in Europe (PDBe)
EMBL Outstation Hinxton +44 (0) 1223 494444 switchboard
European Bioinformatics Institute +44 (0) 1223 494487 fax
Wellcome Trust Genome Campus +44 (0) 1223 494550 helpdesk
Cambridge CB10 1SD UK
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