Hi all, I have a little problem... R and R-free from phenix.refine are 22.9 and 30.6 respectively.... when i validated in the rcsb server... sfcheck gave me a R and Rfree of 30.8 and 37.8. I am aware that sfcheck never reproduces the result. but i am worried that the difference is quite large... indeed i have used TLS NCS and bulk solvent correction... Did i do anything wrong... please help me Thanks for your help regards John
Hi John, my understanding is that SFCHECK does not reproduce the TLS or bulk solvent scaling. Depending on your structure this can be a huge effect on the R-factors. Cheers, Paul On Sep 22, 2008, at 8:35 PM, john kryst wrote:
Hi all, I have a little problem... R and R-free from phenix.refine are 22.9 and 30.6 respectively.... when i validated in the rcsb server... sfcheck gave me a R and Rfree of 30.8 and 37.8. I am aware that sfcheck never reproduces the result. but i am worried that the difference is quite large... indeed i have used TLS NCS and bulk solvent correction...
Did i do anything wrong... please help me
Thanks for your help
regards John _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Kristine Sawyer [ [email protected] ][ 1-510-486-4151 ] --
Hi John, I completely agree with Paul. Just to add that this difference could also be large if you are refining against neutron data. Pavel. On 9/22/2008 9:12 PM, Paul Adams wrote:
Hi John,
my understanding is that SFCHECK does not reproduce the TLS or bulk solvent scaling. Depending on your structure this can be a huge effect on the R-factors.
Cheers, Paul
On Sep 22, 2008, at 8:35 PM, john kryst wrote:
Hi all, I have a little problem... R and R-free from phenix.refine are 22.9 and 30.6 respectively.... when i validated in the rcsb server... sfcheck gave me a R and Rfree of 30.8 and 37.8. I am aware that sfcheck never reproduces the result. but i am worried that the difference is quite large... indeed i have used TLS NCS and bulk solvent correction...
Did i do anything wrong... please help me
Thanks for your help
regards John _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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john kryst
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Paul Adams
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Pavel Afonine