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

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

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

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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

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

I would assume that the wrong chiralities were introduced during building.
It is not very hard to change chiral centers around if you're dragging atoms
around in and out of density...

Artem

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale
Tronrud
Sent: Saturday, August 02, 2008 2:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] D-Amino acids to L-Amino acids

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
>

CCP4bb navigation

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

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

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