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Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034 |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034 From: Mark A Saper saper {- at -} UMICH {- dot -} EDU Date: 2008-01-01 Garib, Many thanks for pointing out the differences. A couple of more questions: 1. Could you tell me how 5.4.0033 by default handled the free and missing reflections in map calculation. Also, is the ccp4i interface suitable for the latest version of refmac --- I add the extra keywords (like anom formfactor) in an "extra-param" file. 2. In version 5.4.0066 version I noticed this line in the log file: Before the second run Unknown atom for fprime and f2prime calculation I didn't receive this error in the older version. Please explain. I'm only specifying f' and f'' for the Selenium. Thanks, Mark On Jan 1, 2008, at 10:29 AM, Garib Murshudov wrote: > Hi Mark > > Could you please try again. > you are right. In case when you gave anom formfactor then f' was > added twice. In this version f' is added correctly. In the previous > version it was added in wrong place. > > Geometry is tighter because we have fixed few bugs related with > chirality and vdw. > > Garib > > > On 1 Jan 2008, at 14:40, Mark A Saper wrote: > >> Thanks for those pointing out my cut and paste error. Below are >> the correct numbers. The first term of the formfactor is almost >> twice as high compared to the other version. I suspect it is >> because the newer version is using the wavelength in the >> calculation, and the old version didn't. >> >> Any help from the authors would be greatly appreciated. >> Mark >> >> Hi, >> >> Well, I guess one shouldn't change versions of refmac in the >> middle of a structure refinement. What are the major differences >> between .0034 and .0066 ? I noted that form factors for the Se >> atom have changed dramatically even though I'm using the same " >> anom formfactor SE -8.13 5.05 " command. Is this because the >> program is now using the wavelength on the .MTZ file ? >> >> with .0034: >> >> SE 8.8706 2.4098 5.8196 0.2726 3.9731 15.2372 >> 4.3543 43.8163 2.8409 >> >> with .0066: >> >> SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 >> 4.3543 43.8163 -11.7969 >> >> The other major difference is that explicit weight that I was >> using = 0.25 is weighting the geometry much more in .0066 compared >> with .0034. Also the refinement is not as well behaved as it was >> in 0.0034. >> >> What has really changed? >> >> Mark >> >> _________________________________ >> Mark A. Saper, Ph.D. >> Associate Professor, Biophysics and Department of Biological >> Chemistry >> University of Michigan >> 3040 Chemistry Building >> 930 N University Ave >> Ann Arbor MI 48109-1055 >> >> saper@umich.edu phone (734) 764-3353 fax (734) >> 764-3323 Research summary >> > _________________________________ Mark A. Saper, Ph.D. Associate Professor, Biophysics and Department of Biological Chemistry University of Michigan 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 saper@umich.edu phone (734) 764-3353 fax (734) 764-3323 Research summary CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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