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Hi Julien - I can't help you with the network question. Maybe you don't have write permissions to the scratch directory on the remote machine? What error messages do you get? As for the R-factor question, it's not unusual to get different values with different programs - sfcheck is probably not using the same solvent model, B-factor correction, and TLS correction that Refmac is using. In particular, the TLS correction usually gives a substantial drop in R factor (compare your CNS output with your Refmac output) but it's not recorded in your PDB coordinates unless you write out anisotropic temperature factors. The difference in R factors is pretty low, and the prettier numbers are what you'll put in the paper anyway. I wouldn't worry about it. A question for the group: is there any push to get TLS parameters incorporated into the standard PDB data format? Right now, the data gets thrown into a comment record where no program really uses it. Even CCP4 programs don't read that information, and refmac has to be given the data in a separate file. - Matt [EMAIL PROTECTED] wrote on 05/18/2006 01:04:47 PM: > *** 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 > > -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
