Clearly a few interesting entries ..... 2) in the context of PX, only the total "B factor" contribution to Fcalc needs to be positive definite, the TLS component might not be (though it is satisfying if it is)
3) how do you calculate the "TLS origin" ? The PDB entries should contain the origin of the coordinate system to which the TLS parameters refer, and thus it is something you choose not something you calculate. You are perhaps comparing the origin used by refmac with the centre of reaction ?? Cheers Martyn -----Original Message----- From: CCP4 bulletin board on behalf of Pavel Afonine Sent: Wed 3/12/2008 10:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB Hi Dale, a few of my observations regarding this issue: 1) A quick run over all TLS containing models in PDB results in this list of models with incorrect TLS selections or other artifacts (see "errors1" file, attached). 2) A lot of reported TLS matrices in PDB are not positive definite. You can easily verify it (I did). 3) Reported TLS origins are not always the same if you compute them yourself (see "errors2" file, attached). This file shows the distance between reported and re-computed TLS origin for each group. 4) Some files contain residual B-factors (Btotal-Btls), and some files contain total B-factors (Bresidual + Btls). ... I have a *very* long list. I re-refine all PDB models (for which data are available) from time to time -:). Let me know if interested. And finally, how you like the anisotropic B-factors in this file -:) http://www.rcsb.org/pdb/files/2atb.pdb Without some prior re-refinement you have almost no chances to reproduce the R-factors for most of these structures. 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/) On 3/12/2008 2:20 PM, Dale Tronrud wrote: > Hi, > > I am looking over a number of models from the PDB but have been > unable to reproduce the R-factors for any model that was refined > with Refmac and contains TLS parameters. I usually can't get within > 5% of the reported value. On the other hand, I usually do pretty > well for models w/o TLS. > > An example is the model 1nkz. The PDB header gives an R value > of 17% but even when I use tlsanal in CCP4i to generate a PDB with > anisotropic B's that mimic the TLS parameters I get an R value of > 22.4% using SFCheck. (I'm not implying that I suspect any problem > with 1nkz, in fact I have every reason to believe this is the great > model its published stats indicate.) > > I've found a CCP4 BB letter that stated that SFCheck does not > pay attention to anisotropic B's but that letter was dated 2002. > I hope this limitation has been removed, or at least the output > would mention this limitation. > > Setting up a refinement in Refmac involves a large overhead, > since even for zero cycles of refinement the program insists on > a complete stereochemical definition for the strange and wondrous > groups in this model. I would just like to verify the R factor > and calculate a proper map for inspection in Coot. Since I have > many models I would like to look at, I would like a simple procedure. > > I did set up a Refmac run for another model, for which I do > have all the .cif's required, but even after refinement I was not > close to the reported R. > > I see that the models I'm interested in are not present in the > Electron Density Server, so I suspect I'm not alone in fighting > this battle. > > Any advice would be appreciated, > Dale Tronrud
