Re: [ccp4bb] homology modeling----good bond lengths, bad angles

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- February 2007 <-- 28 February 2007

Previous message:
Subject: Re: improve crystal size and quality -- membrane protein
From: ddas {- at -} LBL {- dot -} GOV
Date: 2007-02-28

Next message:
Subject: Re: Filament lifetime on Rigaku Micromax007
From: pzhang {- at -} SIBS {- dot -} AC {- dot -} CN
Date: 2007-02-28

Subject: Re: homology modeling----good bond lengths, bad angles
From: leo {- at -} PFWEIS {- dot -} KEK {- dot -} JP
Date: 2007-02-28

Dear Anagha,

just a guess...

I'm not sure I understood you properly, but you are only trying to
make a model of a solved protein which will lack 3-4 amino acids in a
loop... therefore, why not using a modeling soft, such as Coot,
remove the amino acids, and do one run of "Regularize Zone"?? You
might need to renumber your chain once you have removed the amino
acids, but it might work...

just a guess...

Best regards.
Leo

On Mar 1, 2007, at 4:11 AM, anagha gupta wrote:

> Hi CCP4 community!
>
> I have constructed a homology model of a deletion variant of a
> protein whose structure has already been solved. These deletions
> are 3-4 amino acid in length and are in a loop that connects two
> helices. The model structures look good with respect to bond
> lengths in the aforementioned loop region but the bond angles
> (especially Phi and Psi) are very distorted. Ramachandran plot
> suggests the same and some of the amino acids flanking the loop are
> now in the disallowed region.
> I thought one way to avoid this is to delete one amino acid at a
> time and construct the model and use the previous model as the
> template to construct the next model. This is not working very
> well in fixing the wrong angles.
>
> I was wondering if
>
> 1) Anybody out there knows good homology modeling software. I used
> SWISS model and CPH model to create my models. I have heard about
> prime but right now am waiting to get the software .
> 2) Is there a way I can fix the angles if I perform an energy
> minimization of the model.
>
> Suggestions are appreciated.
> Thanks,
> Anagha.

==========================
Chavas Leonard M.G., Ph.D.
Structural Research Center
KEK,PF. 1-1 Oho
Tuskuba, Ibaraki - Japan
---------------------------------------------
PHS: +81(0)29-864-5200 (ext: 2682)
e-mail: leo@pfweis.kek.jp
URL: http://pfweis.kek.jp/~leo
==========================

CCP4bb navigation

CCP4bb <-- 2007 <-- February 2007 <-- 28 February 2007

Previous message:
Subject: Re: improve crystal size and quality -- membrane protein
From: ddas {- at -} LBL {- dot -} GOV
Date: 2007-02-28

Next message:
Subject: Re: Filament lifetime on Rigaku Micromax007
From: pzhang {- at -} SIBS {- dot -} AC {- dot -} CN
Date: 2007-02-28