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