Re: [ccp4bb] unit cell flags in mtz files and refmac

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

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From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-02-27

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Subject: Re: unit cell flags in mtz files and refmac
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-03-02

This is a REFMAC bug; now fixed I believe.. at least in version 82 and
higher..
You can download it from Garibs web site..

Eleanor

Jan Abendroth wrote:
> Hi all,
> I am trying to follow good practices and keep my set of free reflections
> between data sets, eg. in this case between an in-house low resolution and a
> synchrotron high resolution data set. High resolution data from hkl2000 were
> imported through the ccp4i task, keeping the low resolution FreeRs. This mtz
> file contains both unit cells, see below. The refined data set contains only
> one unit cell description, unfortunately the one from the FreeR
> (refmac5.5.72 and refmac5.5.70). As the two unit cells are sufficiently
> different, coot displays the model towards the edge of the density, real
> space refinement pulls the model back in the middle, refmac then starts with
> really high Rs and pulls the model back "out".
>
> When using rather ancient refmac5.2.0019, the mtz file has the correct unit
> cell description.
>
> Btw. both refinements look about the same. The only difference is a rather
> annoying shift of the electron density that is displayed in coot based on
> different unit cell in the mtz file.
>
> Is there a way to tell refmac which of the two unit cells to put in the
> output mtz file? Intuitively, it should be the one from which the amplitudes
> originate?
>
> Cheers
> Jan
>
>
> *mtz file after import*
> 1 myprotein
> high_reso
> synchrotron
> 79.0610 79.0610 311.7950 90.0000 90.0000 90.0000
> 1.00000
> 2 myprotein
> low_resol
> rotating_anode
> 78.5860 78.5860 311.1900 90.0000 90.0000 90.0000
> 1.54180
>
>
> *refmac5.5.0072*
> 2 myprotein
> low_reso
> rotating_anode
> 78.5860 78.5860 311.1900 90.0000 90.0000 90.0000
> 1.54180
>
> *refmac5.2.0019:*
> 1 myprotein
> high_reso
> synchrotron
> 79.0610 79.0610 311.7950 90.0000 90.0000 90.0000
> 1.00000
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: radiation damage
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-02-27

Next message:
Subject: coot crashes
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-03-02