Re: [ccp4bb] coot and stereochemistry

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: ccp4 pdb format
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-03-20

Next message:
Subject: Re: Sketcher and stereochemistry
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20

Subject: Re: coot and stereochemistry
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20

On Tue, 2007-03-20 at 08:57 +0100, Laurent Maveyraud wrote:
> Dear list,
>
> another question related to stereochemistry, but concerning coot.
> When using the RSR zone button, which should "improve geometry and fit to
> map", it seems that the geometry is not always improved : some chiral
> centers can be inverted.

That is not always a bad thing.

> The surprising thing is that using the "regularize
> zone" afterwards does not correct this, even if the chirality of the center
> is not set to both, but to positive in the cif dictionary (ie should define
> only one possible chirality).
> Has anybody else notices this behavior ? Is there a way to adjust the weight
> between geometry and map terms in the RSR option ?

Chiral volumes are not part of the geometric target function in Coot[1],
so changing the weight will have no effect.

Currently what I do for chiral volumes (as a work-around) is use
Validate -> Incorrect Chiral Volumes to find the building errors. They
are trivial to fix when you know where they are. Often I use single
atom drag to move the chiral centre to the other side of the chiral
plane (made by the chiral neighbours).

Paul.

[1] They should be, I tried it but it made the minimization slow and
unstable. I should try it again.

CCP4bb navigation

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

Previous message:
Subject: Re: ccp4 pdb format
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-03-20

Next message:
Subject: Re: Sketcher and stereochemistry
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20