From P.J.Briggs@dl.ac.uk Thu Jun 1 14:15:36 2006 Date: Wed, 31 May 2006 22:36:39 +0100 From: P.J.Briggs To: Martyn Winn , Garib Murshudov Cc: Peter Briggs Subject: Refmac TLS, residual Bs and deposition Hi Martyn & Garib Apologies for the lengthy message. I'm currently at the RCSB PDB and I seem to have walked into something of a controversy over the deposition of REFMAC TLS output PDBs files containing residual B factors. Essentially I have been told that submitting files with residual B factors in ATOM records is not acceptable, and is not migitated by the inclusion of the line: REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY in the PDB header. According to Helen Berman, in the PDB standard the B-factor column of the ATOM records can only contain the full B factors. My understanding is that: 1. REFMAC using TLS refinement outputs residual Bs only, and 2. we have been advising users that it is ok to deposit the PDB file with residual B-factors, without any further processing on their part. If the above is correct, then I know that running TLSANL can restore the total B's as well as producing ANISOU records (which presumably contain the information on the anisotropy modelled by TLS, in a different form). My naive recommendation would be that depositors are therefore advised to run TLSANL with BRESID and ISOOUT FULL keywords prior to deposition, to make a file suitable for deposition. This would seem to be a very simple solution, however: the PDB file output by TLSANL is not the same as the TLS refined file, and I don't know if there are issues which make this inadvisable in practice. So my questions are: 1. Can you clarify if my understanding of the output of residual Bs only from REFMAC with TLS is correct? 2. Can you clarify what users are currently advised to deposit from TLS refinement? 3. Can you tell me if there was there any agreement with the EBI over what TLS data is acceptable for deposition? 4. Can you tell me what the issues might be with advising users to use TLSANL to convert residual Bs to full Bs plus ANISOUs for deposition? I appreciate that this may not be straightforward, and I apologise for cold-calling you on this. Nevertheless, any information that you can provide would be useful to me to clarify the situation. Tomorrow (Thursday) at 11am (4pm UK time) there will be a videoconference between annotators at the RCSB and the EBI, and this issue will be discussed (among others). Thanks for your help, best wishes Pete -- ___________________________________________________ Peter J Briggs, pjx@dl.ac.uk Tel: +44 1925 603826 CCP4, ccp4@dl.ac.uk Fax: +44 1925 603825 http://www.ccp4.ac.uk/ Daresbury Laboratory, Daresbury, Warrington WA4 4AD