[ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Plz suggest me
From: Kornelius Zeth kornelius {- dot -} zeth {- at -} TUEBINGEN {- dot -} MPG {- dot -} DE
Date: 2008-01-01

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From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-01-01

Subject: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Mark A Saper saper {- at -} UMICH {- dot -} EDU
Date: 2008-01-01

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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Plz suggest me
From: Kornelius Zeth kornelius {- dot -} zeth {- at -} TUEBINGEN {- dot -} MPG {- dot -} DE
Date: 2008-01-01

Next message:
Subject: Re: Plz suggest me
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-01-01