Dale, You raise a very important point. The electron density server will not put out the data unless there is a reasonable agreement between the Author reported R-factor and the calculated R-factor. I guess for the same reasons (and more - Gerard?).
The question I have is - if we are going to ask people to deposit data with their model - what information should be deposited (and be in the header of the CIF or PDB file), that would allow us to reproduce the exact maps and statistics that the author reports? We have been struggling with that for some time now in my lab. If the community can come up with an answer, then I am sure we can convince PDB to add those information. Best, Rams. S. Ramaswamy Department of Biochemistry University of Iowa. On Wed, 2008-03-12 at 14:20 -0700, 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
