Re: [ccp4bb] solvent mask with refmac

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

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Subject: Re: solvent mask with refmac
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2009-06-02

Dear Ana-Maria,

in my experience, mask bulk solvent artifacts can only occur at narrow
channels, where the mask radius is too big to define the channel as
belonging to the bulk solvent region, leaving it "empty" and thus
resulting in positive (!) difference density. Changing from simple
scaling to Babinet scaling is an important check to exclude mask bulk
solvent artifacts, but there, you have to uncheck the "calculate
contribution from the solvent region", because this is done by the
Babinet scaling, already.
However, in your case, you have negative difference density in a, as
you say, big cavity. This will be certainly filled with bulk solvent
density. One possible reason for a negative difference density are
underestimated magnitudes of
Fobs
at very low resolution, either
because they are weakened by the beam-stop (half-)shadow, or because
they are overloads that have been poorly extrapolated. A simple check
for wrongly determined low-resolution
Fobs
is to cut your low
resolution data during refinement at a somewhat higher resolution, say
20 A instead of 80 A, and see whether the negative difference density
disappears. If, yes, you should check your data processing again.

Best regards,

Dirk.

Am 02.06.2009 um 10:43 schrieb Ana-Maria Goncalves:

> Dear BB,
>
> I'm refining a structure which presents a big hydrophobic cavity
> where a strong residual difference negative density can be seen. I
> presume that this is an effect of not having a proper solvent mask
> determined and I was wondering if there is a way to provide a better
> mask description to REFMAC. The resolution of the data is 1.6 A and
> I have already tried changing from simple to Babinet scaling,
> without any improvement. Any advice/suggestion would be very welcome.
>
> Many thanks,
> Ana-Maria
>
>
>
> --
> Ana-Maria Goncalves
> Macromolecular Crystallography Group
> European Synchrotron Radiation Facility
> B.P. 220, 6 rue Jules Horowitz
> F-38043 GRENOBLE CEDEX
> FRANCE
>
> Tel: +33 (0) 4.76.88.19.12
> Fax: +33 (0) 4.76.88.29.04

*******************************************************
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: Postdoctoral position at Karolinska Institutet
From: Jodie Guy Jodie {- dot -} Guy {- at -} KI {- dot -} SE
Date: 2009-06-02

Next message:
Subject: PhD studentship (Paris region)
From: Konrad Hinsen hinsen {- at -} CNRS-ORLEANS {- dot -} FR
Date: 2009-06-02