Hi Clement, Refmac actually does write out CCwork and CCfree out in its log files, so you can already check to see whether this you can use these metrics as you propose. We use these values in PDB-REDO to do paired refinement. IMO this is a better way of finding a high-resolution cut-off than going for a specific CC1/2 value. We also write out whether CCfree (and CCwork) have changed significantly over the course of the PDB-REDO run.
Cheers, Robbie From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Clement Degut Sent: Thursday, November 08, 2018 13:05 To: [email protected] Subject: [ccp4bb] CC work / free Hi all, This probably have already be discussed, but can't find trace of it : Is there any reason I am not aware of that refinement software (thinking of both phenix and refmac) do not output CC work / free ? We all accepted CC 1/2 for resolution cut (whether it's 30 or 10 %) which tend to lead to high Rfree ( last shells having very poor phases), at least high overall R free in regard to the majority same resolution structures as they been refined with I/sig > 3. Which in return push people to cut resolution AFTER refinement which obviously drastically decrease the R free and catapult your structure from worst of the PDB to best of the PDB. It should never be done but it is nonetheless. How to blame a "non expert" to do that when changing the resolution from 1.49 to 1.5 change your Rfree by 2% (yes it exaggerated but you get the idea). Now it seems to me -but I may be very wrong as I am far from expert in the arcane math of these- that CC work and free would be more agnostic to this resolution cut off problem, as we compare it to the CC* value anyway ? thought it will never start to be used if refinement software don't output it as a standard (not talking about completely replacing Rfree here as it is obviously useful). Would CC work/free be a bad appreciation of the refinement process ? Thanks Clément ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
