Re: [ccp4bb] Phaser question

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

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Subject: Re: Software for predicting potential disulfide cross-linking sites?
From: Bart Hazes Bart {- dot -} Hazes {- at -} UALBERTA {- dot -} CA
Date: 2009-09-30

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From: Leslie Kinsland lk65 {- at -} CORNELL {- dot -} EDU
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Subject: Re: Phaser question
From: Randy Read rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2009-09-30

In a Phaser automated molecular replacement job, it does almost
everything at a working resolution and then a final refinement at a
final resolution. By default, the working resolution is 2.5A and the
final resolution is the full resolution of the data set. So the
second-last LLG is the one computed with the working data (probably to
2.5A) and the last one is the LLG computed with all the data. Both
LLG values are after rigid-body refinement.

If the final LLG goes negative, then this probably means that the
model isn't as good as Phaser was assuming, and that this becomes a
problem in particular for the data at higher resolution.

Best wishes,

Randy Read

On 30 Sep 2009, at 16:50, Simon Kolstoe wrote:

> Dear all,
>
> In the phaser .sol file what do the two LLG's correspond to on the
> SOLU SET line eg
>
> SOLU SET RFZ=20.7 TFZ=35.4 PAK=0 LLG=1699 LLG=2821
>
> Do they show an initial and a refined LLG or do they correspond to
> the rotation and translation function as in the Z scores?
>
> I checked the appropriate web page and didn't see anything immediate.
>
> http://www-structmed.cimr.cam.ac.uk/phaser/documentation/phaser-2.1_key.html#MR_solved_it
>
> Thanks,
>
> Simon

------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: rjr27@cam.ac.uk
Cambridge CB2 0XY, U.K. www-
structmed.cimr.cam.ac.uk

CCP4bb navigation

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

Previous message:
Subject: Re: Software for predicting potential disulfide cross-linking sites?
From: Bart Hazes Bart {- dot -} Hazes {- at -} UALBERTA {- dot -} CA
Date: 2009-09-30

Next message:
Subject: Peter Boyd, RIP
From: Leslie Kinsland lk65 {- at -} CORNELL {- dot -} EDU
Date: 2009-09-30