Hi, I have done a couple of refinements using either phenix.refine 1.3-rc4 or phenix.refine 1.3-final. And phenix.refine 1.3-rc4 always gave me a lower Rfree, about 1% lower than phenix.refine 1.3-final, which actually is pretty big. What has changed between this two versions? -- Jianghai
Hi Jianghai, Pavel introduced an automatic modification of the weights between these two versions. In general it is an improvement but in some cases the final R-factors can be a bit higher than using fixed weights. Unfortunately there isn't a way to turn off this autoweighting in 1.3- final. Pavel will add this option and we'll release an updated installer soon (there are a couple of other bugs we've found elsewhere in PHENIX that are being fixed also). Cheers, Paul On Sep 11, 2008, at 7:54 AM, Jianghai Zhu wrote:
Hi,
I have done a couple of refinements using either phenix.refine 1.3-rc4 or phenix.refine 1.3-final. And phenix.refine 1.3-rc4 always gave me a lower Rfree, about 1% lower than phenix.refine 1.3-final, which actually is pretty big. What has changed between this two versions?
-- Jianghai
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-- 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: 510-486-4225, Fax: 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 ] --
Is the option to turn off automatic weighting available in the new 2008_09_13_0905 CCI apps? -- Jianghai On Sep 11, 2008, at 11:58 AM, Paul Adams wrote:
Hi Jianghai,
Pavel introduced an automatic modification of the weights between these two versions. In general it is an improvement but in some cases the final R-factors can be a bit higher than using fixed weights. Unfortunately there isn't a way to turn off this autoweighting in 1.3- final. Pavel will add this option and we'll release an updated installer soon (there are a couple of other bugs we've found elsewhere in PHENIX that are being fixed also).
Cheers, Paul
On Sep 11, 2008, at 7:54 AM, Jianghai Zhu wrote:
Hi,
I have done a couple of refinements using either phenix.refine 1.3- rc4 or phenix.refine 1.3-final. And phenix.refine 1.3-rc4 always gave me a lower Rfree, about 1% lower than phenix.refine 1.3-final, which actually is pretty big. What has changed between this two versions?
-- Jianghai
_______________________________________________ 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: 510-486-4225, Fax: 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 ] --
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Hi,
currently you cannot turn off automatic weights adjustement. I will add this option once I'm back to work.
Also, could you please explaine why you need it? If current version of phenix.refine results in problems could you send me the reproducer. I'm asking this because normally you don't need to turn it off?
Cheers,
Pavel.
----- Original Message -----
From: "Ralf W. Grosse-Kunstleve"
Is the option to turn off automatic weighting available in the new 2008_09_13_0905 CCI apps?
Nope. Sorry. Pavel is out of town until the end of this month. It will only happen after he is back. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Jianghai Zhu -
Paul Adams -
Pavel Afonine -
Ralf W. Grosse-Kunstleve