Re: [ccp4bb] pdb file deposition

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

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- X-ray detectors

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

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Subject: pdb file deposition
From: Azadeh Shahsavar azadeh {- dot -} shahsavar {- at -} GMAIL {- dot -} COM
Date: 2010-03-11

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Subject: Re: pdb file deposition
From: Kevin Jude kjude {- at -} BERKELEY {- dot -} EDU
Date: 2010-03-11

Probably, you have built water molecules that are associated with
symmetry-related macromolecules rather than the host molecule. Turn
symmetry on, check the nearest neighbors of the offending waters, and move
the waters close to the host molecule if appropriate. I believe you can do
this with the CCP4 program watertidy.

kmj

On Thu, Mar 11, 2010 at 12:15 PM, Azadeh Shahsavar <
azadeh.shahsavar@gmail.com> wrote:

> Dear All,
>
> In depositing a pdb file, after validation step, an error comes up:
> *Solvent Atoms* The following solvent molecules lie farther than expected
> from the protein.
>
> Can any one give me some advice about it?
> deleting these water molecules results in a large increase of R factor, by
> the way.
>
> Thank you in advance,
>
> A
>

CCP4bb navigation

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

Previous message:
Subject: pdb file deposition
From: Azadeh Shahsavar azadeh {- dot -} shahsavar {- at -} GMAIL {- dot -} COM
Date: 2010-03-11