Re: [ccp4bb] D-Amino acids to L-Amino acids

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

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Subject: Re: Rotation axis
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-08-03

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From: "Borhani, David" David {- dot -} Borhani {- at -} DESHAWRESEARCH {- dot -} COM
Date: 2008-08-04

Subject: Re: D-Amino acids to L-Amino acids
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-08-03

Yusuf Akhter wrote:
> Hi Everybody,
>
> I am refining structure of a protein at 3 Angstrom. I am doing model building in
> Coot.
> After several rounds of refinement using Refmac when I tried to run PROCHECK on
> my partially build model I found that some of the residues are D-amino acids.
>
> How to change these D-amino acids to L-amino acids??

> Is there any option in Coot for that??

Use Coot 0.4.x or better and the situation would not occur (IIUC).

To fix the problem you have, use Coot 0.4.x or better and use the
incorrect chiral volume diagnostic and then RSR or regularize the
affected AA.

Other than that, I would agree with Dale Tronrud.

Paul.

CCP4bb navigation

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

Previous message:
Subject: Re: Rotation axis
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-08-03

Next message:
Subject: Re: Rotation axis
From: "Borhani, David" David {- dot -} Borhani {- at -} DESHAWRESEARCH {- dot -} COM
Date: 2008-08-04