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Hi, the temperature factors after refmac5 with TLS only contains the isotropic contribution (hope this is put correctly). If you want to use sfcheck on that file, you probably want to use the PDB-file written by tlsanl - it makes the atoms anisotropic to describe the TLS-refinement more correctly. I reckon that refmac5 does not write out the atoms anisotropically directly because other programs may not know that the atoms are not independently anisotropic but link within the groups. -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 18 May 2006, Julien Lafrance-Vanasse wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi > > Sorry for these real-ccp4 questions: > > 1. Remote jobs > I tried to run a remote job on a distant computer. It didn't work. I guess > it has to run on a local network with the /home and /tmp shared by NFS?!? > Does anyone has a script integrated in ccp4 that transfers file to another > machine, runs the job and re-transfers the ouput? > > 2. R and r_free under REFMAC > I decided to run refmac with TLS at the end of my refinement process. I'm > quite new to ccp4, because I usually use cns. The conversion between the two > went well. > > I ran SFcheck on the initial model, to mesure r and free_r which gives > 0.186/0.208. There's a small difference with cns (0.1854/0.2060), but that > doesn't bother. What really bothers is those values at the end of the > refinement with REFMAC. The values go down during the refinement process (if > I look at the log graph) and the pdb output gives: > REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT > REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM > REMARK 3 R VALUE (WORKING + TEST SET) : 0.16981 > REMARK 3 R VALUE (WORKING SET) : 0.16822 > REMARK 3 FREE R VALUE : 0.20006 > REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 > REMARK 3 FREE R VALUE TEST SET COUNT : 8921 > > But if I run SFcheck on the output pdb, it gives me 0.187/0.217, which is > approx 0.02 difference with REFMAC! I really don't understand what happens. > I'm asking myself if the refinement went well and from two programs, I have > different values! > > Thank you, > > Julien > >
