From garib@ysbl.york.ac.uk Thu Jun 1 14:15:59 2006 Date: Wed, 31 May 2006 23:22:26 +0100 From: Garib Murshudov To: P.J.Briggs Cc: m.d.winn@dl.ac.uk Subject: Re: Refmac TLS, residual Bs and deposition Hi Pete I had some discussions about TLS with Kim Henrick I will send you a bit more to clarify situation Meanwhile: 1) REFMAC outputs residual B values and there are TLS description with in mmCIF format and it was doen with EBI together. 2) Users deposit TLS parameters as well as residual B values. If they use deposition files then they deposit TLS parameters in mmCIF format. That is what is adivsed 3) Description of TLS was done together with EBI. But still there are some confusions. 4) Deposting full aniso does not reflect model used. It may be stop-gap solution but I am afraid if this path is taken then there might be even more confusion in future Garib On Wed, May 31, 2006 at 10:36:39PM +0100, P.J.Briggs wrote: > > 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 > -- ------------------------------------------------------------------ Garib N. Murshudov, Chemistry Department, University of York, U.K. Tel: Home +44 (1904) 32 82 52, work: +44 (1904) 43 25 65 ------------------------------------------------------------------