I think that it is essential that the PDB file that actually gets deposited contains ANISOU records that have had the isotropic contributions added already, and that the B on the atom record is one third of the trace of the orthogonalised Bij tensor that can be derived from the ANISOU record, just as it is for an anisotropic refinement without TLS (or a refinement with TLS restraints rather than constraints, as in the next version of SHELXL, release NOT imminent). Then if you are not interested in anisotropy you still have meaningful B values on the ATOM record, and a structure factor calculation (e.g. with SFCALC) will get the R factors right. If I have understood the rather convoluted discussion on this question, phenix.refine does this correctly, but if you use REFMAC you need to use another program (TLSANL ?) to convert the PDB file before you deposit it. Apparantly many people have forgotten to do this and the RCSB/EBI has unfortunately not checked it (which would be trivial for them to do). If they could be persuaded to check that the ATOM and ANISOU records are consistent as explained above, the problem would sort itself out, at least for new depositions.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Sat, 29 Mar 2008, Pavel Afonine wrote: > Hi Frank, > Hi Frank, > > > All your reasons are there for the convenience of the *crystallographer*, > > mine are for the end user (=unsuspecting biologist) -- who doesn't know TLS > > even exists (none of used to), never mind about Hirshfeld's test and how it > > relates to TLS (I didn't), and certainly not how run it (I still don't). > > > > This is exactly what phenix.refine does: it puts all together so you are not > expected to have any knowledge about magic TLS matrices in PDB file header, > about right programs to convert one into another and so on. In contrast, if > one split things apart: > - you must know that what's in ATOM record is incomplete; > - you must know that there are TLS matrices that you have to convert to > appropriate B and add to residual ones; > - you must know that there are the programs out there to do that; > - and you must know how to use these programs too. > > So, having complete record doesn't require any manipulations on the model (and > so extra knowledge) . > > Imagine the situation when you got a model with partial B-factors and another > part encoded in PDB header as TLS and you want to do a refinement in SHELXL. > In this case you will need to compute the total B to start with the correct > values. In contrast, if the values are complete, you do not need to do > anything. > > In the end what's important I believe is that the output information is > clearly accompanied with the explanations about what it represents and that > there are tools available from both ends (phenix, ccp4) to easily go from > partial to total and back. The rest is the matter of personal preferences. > > Cheers, > Pavel. > --- > Pavel V. Afonine, Ph.D. > Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/) > CCI: Computational Crystallography Initiative (http://cci.lbl.gov/) > PHENIX (http://phenix-online.org/) > >
