Re: [ccp4bb] How to refine a solution obtained by molecular replacement

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

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Subject: Beam time available @X6A NSLS
From: "Stojanoff, Vivian" stojanof {- at -} BNL {- dot -} GOV
Date: 2009-03-17

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Subject: Re: How to refine a solution obtained by molecular replacement
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-03-17

Dear Sun,

if I remember correctly phaser already carries out a rigid body refinement
of its solution.

To avoid and remove as much model bias as possible, I suggest you look at
the solution from phaser and build _as_ _much_ _as_ _possible_ BEFORE you
do any further refinement, i.e., try to match the sequence, correct side
chains, etc. Only once you cannot do any bettermanually you should run a
refinement program and after that again build as much as possible, etc.

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

On Tue, 17 Mar 2009, Sun Tang wrote:

> Dear All,
>
> Recently I solved a structure at 2.5 A with PHASER, with two molecules in
> assymetric unit. There are no short contacts in the solution. However,
> the Rfree stays at about 50% after the refinement of rigid boby and
> restrained refinement in CNS. The sequences homology is about 30%.
>
> What is the usual way to deal with this kind of problems? Should I just
> refine the backbone of the structure and then build the side chains?
>
> Your suggestions are greatly appreciated!!!
>
> Best wishes,
>
> Sun
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Beam time available @X6A NSLS
From: "Stojanoff, Vivian" stojanof {- at -} BNL {- dot -} GOV
Date: 2009-03-17

Next message:
Subject: Job
From: Sergiy Klyuyev klyuyev {- at -} UAB {- dot -} EDU
Date: 2009-03-17