[ccp4bb] High R factor
Dear Sir/Madam, I am very new to this CCP4 program. Usually I know that after rigid body refinement the R factor reduces from the R factor what ever we get from Molrep. One of my data is showing some different characteristics. After running Molrep the R factor is showing 38% and score is 64%, but when I run rigid body refinement (Refmac5) the Rfactor is showing 46.07% and Rfree is 46.27. is it possible? Or else what I have to do with this data. Please suggest. Regards Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] High R factor
Hi, it might well be possible that molrep used only lower resolution data (the default cutoff isd 2.5 A, if I remember correctly), when refmac uses all available data in the MTZ file... Check that both steps were performed at the same resolution ! Another possibility is that molrep performed the search in different spacegroups than the one specified in the MTZ file (eg P4 selected during data processing, and molrep checks, P4, P41, P42 and P43). If your solution corresponds to the P41 spacegroup, you have to modify your MTZ file (or use the one produced by molrep)... otherwise refmac will perform the rigid body step in P4 and not P41... This should be indicated in the molrep logfile... check it carefully ! hope this helps. If not please send the logfiles ! Laurent Le 20/02/2012 11:48, Dipankar Manna a écrit : Dear Sir/Madam, I am very new to this CCP4 program. Usually I know that after rigid body refinement the R factor reduces from the R factor what ever we get from Molrep. One of my data is showing some different characteristics. After running Molrep the R factor is showing 38% and score is 64%, but when I run rigid body refinement (Refmac5) the Rfactor is showing 46.07% and Rfree is 46.27. is it possible? Or else what I have to do with this data. Please suggest. Regards Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
[ccp4bb] high R factor calculated by sfcheck
Dear all, I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result). But when I used sfcheck to validate the coordinates and structure factors, I got a high R factor > 0.38 ! Could anybody tell me the reason? Is that possible to deposit the coordinate to PDB? Thank you very much!
Re: [ccp4bb] high R factor calculated by sfcheck
On Mon, 2012-04-23 at 23:39 +0800, Qixu Cai wrote: > Dear all, > > I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result). > But when I used sfcheck to validate the coordinates and structure factors, I > got a high R factor > 0.38 ! > > Could anybody tell me the reason? Is that possible to deposit the coordinate > to PDB? > > Thank you very much! There are differences between the two programs. For instance, sfcheck uses Babinet solvent correction, while Refmac's default is to use mask correction. Perhaps you used TLS, which sfcheck is not likely to use. You do have a relatively large jump, but it's not entirely unexpected given the resolution. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
