Re: [ccp4bb] solvent mask with refmac

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

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Subject: precipitation of the protein in crystallisation solution
From: peter hudson peter {- dot -} hudson {- dot -} peter {- at -} GMAIL {- dot -} COM
Date: 2009-06-02

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Subject: Re: solvent mask with refmac
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-06-02

On Tue, Jun 02, 2009 at 12:57:59PM -0400, Ed Pozharski wrote:
> I've seen this before in some structures and have verified in those
> cases that correction of the bulk solvent mask fixes the negative
> density.
> ...
> It was quite convincing that it's indeed empty cavities large enough
> to be filled with artifact bulk solvent.

We do that by default in BUSTER now for ~5 years - also with good
experiences (all assuming the data isn't particularly weird at the low
resolution end - as discussed by others).

> In general, my experience was that although the negative density
> disappears, effect on R/Rfree is negligible (less than 0.1%). They seem
> to be cavities made exclusively out of hydrophobic sidechains (i.e.
> carbon-only), but may set of observations is, of course, limited.

We see very rarely an increase in R/Rfree - but this nearly always
points back to very poor data and/or extremely partial models. In the
vast majority it doesn't hurt at all and in a lot of cases it gives
some significant drop in Rfree (0.5%) and/or reduction of Rfree-R
gap. But the nicest thing is: it makes looking at those Fo-Fc maps so
much easier - you don't get distracted by negative difference density
caused by wrong bulks solvent modeling.

Cheers

Clemens

--

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* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
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CCP4bb navigation

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

Previous message:
Subject: precipitation of the protein in crystallisation solution
From: peter hudson peter {- dot -} hudson {- dot -} peter {- at -} GMAIL {- dot -} COM
Date: 2009-06-02

Next message:
Subject: Beamtime at Cornell High Energy Synchrotron Source
From: Marian Szebenyi dms35 {- at -} CORNELL {- dot -} EDU
Date: 2009-06-02