Re: [ccp4bb] PHENIX & BSS refinement

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

Previous message:
Subject: Re: correlation length - reloaded
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-02-03

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Subject: Obtaining relationships between two cross rotation solutions?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-02-03

Subject: Re: PHENIX & BSS refinement
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2009-02-03

Hi Jose,

> We have seen that the recent versions of phenix (1.3) the structure
> refinement ends with a bulk solvent correction step, something I found
> quite unusual (absent in other refinement programs and in older
> versions of phenix, 1.24.1).

- the software is evolving and gets better over time -:) That is,
version 1.3 is supposed to be better than 1.24.1, and the latest 1.4
should be better than 1.3.

- it is good to update bulk solvent correction at the end of refinement.
For example, the refinement of coordinates may invalidate the mask which
in turn invalidates the solvent contribution Fbulk.

> We have also seen that the B factor jumps up in this last step (see
> bellow). Is anybody aware of this?

This is because the trace of overall anisotropic scale matrix is added
to atomic B-factors and subtracted from that matrix. This is exactly
what CNS does (at least version 1.1).

> Do you know how to get rid of this final bss step?

It is not a good idea, so phenix.refine does not have an option to turn
it off.

> This step is redundant, as bss is also done at the beginning of each
> ref cycle.

It is not redundant: see above.

FYI: there is PHENIX bulletin board:
http://www.phenix-online.org/mailman/listinfo/phenixbb

Pavel.

CCP4bb navigation

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

Previous message:
Subject: Re: correlation length - reloaded
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-02-03

Next message:
Subject: Obtaining relationships between two cross rotation solutions?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-02-03