Re: [ccp4bb] Squashed density

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

Previous message:
Subject: Squashed density
From: "Kolstoe S {- dot -} E {- dot -} " S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-06-27

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Subject: Post Doc Fellow (Computational Crystallography Initiative) at LBNL, Berkeley, CA
From: Amy Pagsolingan avpagsolingan {- at -} LBL {- dot -} GOV
Date: 2007-06-27

Subject: Re: Squashed density
From: Miguel_Ortiz-Lombardía ibdeno {- at -} GMAIL {- dot -} COM
Date: 2007-06-27

Hi Simon,

What graphics program are you using to inspect the density? Are you reading
in directly the maps produced by CNS or converting them to some other
format? If you convert it, the most likely culprit is the conversion
procedure...

Miguel

2007/6/27, Kolstoe S.E. :
>
> Dear CCP4 message board,
>
> I am having a problem with electron density that looks as if it has been
> compressed along the Y axis. Density that would appear as a sphere looks
> like an ellipsoid, and the effect seems worse in some regions (typically
> where I am having problems building in a flexible loop). It is worse in my
> Fo-Fc map (compared to my 2Fo-Fc) which makes me wonder if there is a
> problem with my calculated F's?
>
> Does anyone know of common reasons for seeing this effect, and how to fix
> it?
>
> (I processed the data in Mosflm, scaled in Scala, phased in phaser and
> then used the usf program dataman to pick my R free set and convert to cns
> format, and have been using anneal, minimize and model_map in CNS).
>
> Simon
>
>

--
correo-e: ibdeno@gmail.com
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CCP4bb navigation

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

Previous message:
Subject: Squashed density
From: "Kolstoe S {- dot -} E {- dot -} " S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-06-27

Next message:
Subject: Post Doc Fellow (Computational Crystallography Initiative) at LBNL, Berkeley, CA
From: Amy Pagsolingan avpagsolingan {- at -} LBL {- dot -} GOV
Date: 2007-06-27