Re: [ccp4bb] Check the conformation of one important amino acid

- Protein crystallography

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

Previous message:
Subject: Re: Check the conformation of one important amino acid
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-02-18

Next message:
Subject: Re: Check the conformation of one important amino acid
From: Miles Pufall mpufall {- at -} CMP {- dot -} UCSF {- dot -} EDU
Date: 2008-02-19

Subject: Re: Check the conformation of one important amino acid
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-02-19

Chavas Leo wrote:

> Dear Sun --
>
>> I want to check the conformation of one important amino acid in the
>> structure by looking the difference density map. Should I just omit
>> that amino acid in the refinement or should I also omit its flanking
>> amino acids? Which one is better?
>
>
> The real expert will talk better than me, but I'd go for removing 1-2
> additional residues around your target. Personal preferences though...
> Depends on your resolution as well. If at low resolution you remove 3
> residues, you might have all of them gone for good, so the target
> would be enough...
>
And then in addition running a composite omit map with CNS.

Good luck,

Jürgen

> HTH
>
> Kind regards.
>
> Leo
> ------------------------------------------------------------
> Chavas Leonard, Ph.D.
> Research Associate
> ------------------------------------------------------------
> Faculty of Life Sciences
> The University of Manchester
> The Michael Smith Building
> Oxford Road
> Manchester Lancashire
> M13 9PT
> ------------------------------------------------------------
> Tel: +44(0)161-275-1586
> e-mail: Leonard.Chavas@manchester.ac.uk
>
>
>

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

CCP4bb navigation

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

Previous message:
Subject: Re: Check the conformation of one important amino acid
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-02-18

Next message:
Subject: Re: Check the conformation of one important amino acid
From: Miles Pufall mpufall {- at -} CMP {- dot -} UCSF {- dot -} EDU
Date: 2008-02-19