[ccp4bb] Default anisotropic B-factor refinement in phenix.refine?!

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

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Subject: Re: educational opportunity: Difference between SIRAS and SAD?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-02-19

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Subject: Re: educational opportunity: Difference between SIRAS and SAD?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-02-19

Subject: Default anisotropic B-factor refinement in phenix.refine?!
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2009-02-19

Dear CCP4ers and phenix developers,

although, this is not the phenix mailing list, this might still be
useful for users as a pointer and for the developers of phenix for,
maybe, improving phenix.

If you refine a macromolecular structure with phenix.refine using TLS
and isotropic B-factors, the resulting PDB file will have the
effective isotropic B-factors and their anisotropic corrections as
ANISOU cards from both the TLS components and the individual isotropic
B-factor component. I think, this is very useful, because the PDB file
has the informations about the various B-factor components readily
available, both for non-crystallographers that are not aware of TLS
and for reproducing refinement results with other software.

However, if such a PDB file is fed into another refinement run with
phenix.refine, the program recognizes the ANISOU cards and
automatically switches to individual anisotropic B-factor refinement,
unless you explicitly state, that you wish to continue with isotropic
B-factor refinement by giving, for instance, a command line keyword
like adp.individual.isotropic=all or convert_to_isotropic=true (see
here).

I think, this is not reasonable, since the vast majority of
macromolecular structures is refined at resolutions that do not
justify anisotropic B-factor refinement, and most users simply use the
default refinement parameters and are probably not aware of this
behaviour.

May I therefore suggest to the developers of phenix to revert this
behaviour, such that isotropic B-factor refinement is the default and
anisotropic B-factor refinement is only done, if the user explicitly
states that she/he wants it?

Best regards,

Dirk.

*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostrewa@lmb.uni-muenchen.de
*******************************************************

CCP4bb navigation

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

Previous message:
Subject: Re: educational opportunity: Difference between SIRAS and SAD?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-02-19

Next message:
Subject: Re: educational opportunity: Difference between SIRAS and SAD?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-02-19