[ccp4bb] Problem with VDW restraints in Refmac

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

Previous message:
Subject: The importance of USING our validation tools
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-08-16

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Subject: Re: The importance of USING our validation tools
From: "Green, Todd" green {- at -} CBSE {- dot -} UAB {- dot -} EDU
Date: 2007-08-16

Subject: Problem with VDW restraints in Refmac
From: Alastair McEwen alastair {- at -} TITUS {- dot -} U-STRASBG {- dot -} FR
Date: 2007-08-16

Dear all,

I am refining a structure with a partially
occupied ligand. The binding site contains a
Glutamine residue with a dual conformation with
the ‘B’ conformation overlapping with the ligand.
I have named the ligand ‘ALIG’ but when refining,
Refmac notes a number of VDW deviations and the
ligand and side-chain are moved away from each
other and out of the density. When I refine
without VDW restraints the ligand and side-chain
refine well in the density but I would like to be
able to use these restraints for the rest of the
structure. Is it possible to have Refmac ignore
these restraints just for this ligand and residue?

Many thanks,

Alastair

Dr. Alastair McEwen
Département de Biologie et Génomique Structurales
IGBMC, 1 rue Laurent Fries, BP10142
67404 ILLKIRCH, France
Tel: +33 (0)3 88 65 57 73
Fax: +33 (0)3 88 65 32 76
email: alastair@igbmc.u-strasbg.fr

CCP4bb navigation

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

Previous message:
Subject: The importance of USING our validation tools
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-08-16

Next message:
Subject: Re: The importance of USING our validation tools
From: "Green, Todd" green {- at -} CBSE {- dot -} UAB {- dot -} EDU
Date: 2007-08-16