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Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034 |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 01 January 2008Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034 From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-01-01 I usually add extra keywords in the "developers option" section of the interface. I hope we will soon change the interface ti suite current and the next version of the program. If unobserved reflections are present in the mtz file with missing reflection flag then for map coefficients they are replaced by DFp. It meant to b statistically more valid and reflect the extected electron density. If they are not present then nothing is done. You can of course remove them from map calculations using sigma in FFT calculation. In the new version for all atoms f' and f'' are calculated. Although only f' is used. If you give anom formfactor for a given atom then it is used (at least it is the idea). f' added to formfactors if the value is more than 0.01. Otherwise they are not considered as anomolous scatterer. In the older version these values were not calculated and used if you gave them or used as if waverlength were CuKa edge. I have to look and see why "Unknown atom for fpriem ad f2prime calculation" is printed. Regards Garib On 1 Jan 2008, at 16:16, Mark A Saper wrote: > 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 <-- 2008 <-- January 2008 <-- 01 January 2008 |
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