Thanks, everybody. I think i fix the problem. I just either phased or autobuilt with the original mtz file (phaser.1.mtz) creating new free r flags. Now the r-work and r-free separate (0.1859 and 0.2104 respectively).
Kindest regards, Tung Dinh PhD student The University of Georgia Department of Chemistry ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tristan Croll <ti...@cam.ac.uk> Sent: Friday, August 30, 2019 12:11:21 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal? [External Sender] ... although this raises a question: if there are no free reflections, then why is a "Rfree" score being reported at all? On 2019-08-30 16:53, Christian Roth wrote: > No. As pointed out by Pavel, there are no reflections flagged as > "free reflections" used to calculate Rfree. Therefore you don't get a > real Rfree. No model bias issue etc. If you have a Rfree using ccp4 > programs, than you should used that particular original mtz in phenix. > It should detect the flagged "free reflections" automatically. > > Cheers > Christian > > On Fri, Aug 30, 2019 at 5:24 PM Tung Thanh Dinh <ttd79...@uga.edu> > wrote: > >> I have been using elipsoidal truncated data all long. And at first i >> couldn't find a well homologous model (50% homology is the best i >> can find) so I use Mr Bump and Buccaneer to create a model to phase >> and autobuild. After a lot of refinement I obtained "good" model >> with good statistics. Then I used this "good" model to either phase >> and autobuild again. So this may be due to the model bias? >> >> Kindest regards, >> Tung Dinh >> >> PhD student >> The University of Georgia >> Department of Chemistry >> ------------------------- >> >> FROM: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tung >> Thanh Dinh <ttd79...@uga.edu> >> SENT: Friday, August 30, 2019 9:36:58 AM >> TO: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> SUBJECT: [ccp4bb] I am doing phenix refinement now. Is it a problem >> if the r-work and r-free values are equal? >> >> After phasing with phenix, i clicked on the phenix.refine ribbon. >> Since then for every macrocycle of refinement, r-work and r-free >> values are always the same. Is this a problem that I need to fix? >> >> Kindest regards, >> Tung Dinh >> >> PhD student >> The University of Georgia >> Department of Chemistry >> >> ------------------------- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 [1] >> >> ------------------------- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 [1] > > ------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 [2] > > Links: > ------ > [1] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > [2] 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
