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

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

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

Previous message:
Subject: Re: D-Amino acids to L-Amino acids
From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-08-02

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Subject: Re: D-Amino acids to L-Amino acids
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-08-02

Subject: Re: D-Amino acids to L-Amino acids
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-08-02

First you should look into why your chiral centers flipped. In
my experience the most common cause is that the neighboring peptide
bond needs to be flipped.

If you just want to flip a chiral center in Coot, I think the
easiest way is to "real space refine" the residue and before accepting
the result, drag the CA to the side you want. You may have over-drag
to get it to stay. It only takes a moment.

But don't assume that your refinement program is just doing something
stupid. Look for the primal cause.

Dale Tronrud

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??
>
>
> Thanks in advance,
> yusuf
>

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

Previous message:
Subject: Re: D-Amino acids to L-Amino acids
From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-08-02

Next message:
Subject: Re: D-Amino acids to L-Amino acids
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-08-02