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Thanks for clearing that up. One thing I might mention is that I found if you run refmac with restrained refinement only (not TLS & restrained refinement) and select "input fixed TLS parameter", then the input TLS parameters don't make it to the header of the output pdb. It says: REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL I guess it makes sense the tensors wouldn't make it to the header since they're not being refined, but that seems like something that should be included. Should add the TLS tensors after the fact to the output PDB? Thanks, Eric On 12/7/06, Ethan Merritt <[EMAIL PROTECTED]> wrote:
On Thursday 07 December 2006 07:04 am, D. Eric Dollins wrote: > I have refined several structures with > restrained refinement with TLS refinement in refmac. If I understand > it correctly, the B-factors listed in the output PDB are residual > Bfactors. Correct > That being said, I deposited the refmac outputted PDB > directly (with Bs as listed) and now I wonder if that was the correct > thing to do. It was, so long as you also deposited the header records that describe the TLS model itself. > What will happen, for example, if and when someone tries > to download the PDB and structure factors to look at the maps using > the electron density server or similiar? Also, the PDB staff told me > that SFCheck is having problems with one of my PDBs (says it has high > Rfactors, when the output Rs from refmac are in the high 20s). Could > the SFCheck be having issues because of the residual Bs? I might we > say significant drop in Rs using TLS refinement. The fact that older programs do not handle TLS models correctly is a problem, but not one you can solve individually. The programs need to be made smarter, or replaced by newer programs. sfcheck in particular is not very good about calculating its own Fcalc. It ignores TLS models, as you note, but also fails to deal with any other non-standard component of the model (contributions from partial Fc's, alternative solvent models, etc). You can safely ignore that aspect of the sfcheck report so long as you have performed the equivalent checks yourself using the "real" Fcalc values. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle WA
-- D. Eric Dollins C266 LSRC, Box 3813 Duke University Medical Center Durham, NC 27710 (919)681-1668
