Re: [ccp4bb] structure validation tools

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

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

Previous message:
Subject: Re: align DNA structures
From: Mark Brooks mark {- dot -} brooks {- at -} U-PSUD {- dot -} FR
Date: 2009-10-21

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Subject: Re: Colored proteins :)
From: Parthasarathy Sampathkumar spartha2 {- at -} GMAIL {- dot -} COM
Date: 2009-10-21

Subject: Re: structure validation tools
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2009-10-21

On Wed, Oct 21, 2009 at 6:20 AM, Katja Schleider wrote:

> I solved my first crystalstructure and now want to publish it. But how do I
> know the structure is ready for publication and deposition in the pdb. We
> can explain our theory with the structure but which factors I have to regard
> to publish nothing wrong or bad. Can anybody tell how many outliers are
> allowed as long as they are in a well defined density?

The Molprobity server suggests the following:

< 0.2% Ramachandran outliers
> 98% Ramachandran favored
< 1% Rotamer outliers
< 1% of residues with bad bonds
< 0.5% of residues with bad angles

(and the clashscore should be as low as possible.)

-Nat

CCP4bb navigation

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

Previous message:
Subject: Re: align DNA structures
From: Mark Brooks mark {- dot -} brooks {- at -} U-PSUD {- dot -} FR
Date: 2009-10-21

Next message:
Subject: Re: Colored proteins :)
From: Parthasarathy Sampathkumar spartha2 {- at -} GMAIL {- dot -} COM
Date: 2009-10-21