Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

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CCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007

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Subject: Re: CNS v1.2 and unwanted introduction of OXT
From: James Irving irving {- dot -} james {- at -} GMAIL {- dot -} COM
Date: 2007-03-05

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From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-05

Subject: Re: CNS v1.2 and unwanted introduction of OXT
From: "Fred {- dot -} Vellieux" vellieux {- at -} IBS {- dot -} FR
Date: 2007-03-05

On Mon, 5 Mar 2007, James Irving wrote:

> Hi Fred,
>
> From memory, this can occur due to long bond lengths in the model being
> interpreted as chain breaks, try editing the generate.inp or
> generate_easy.inp script and increase the value for "break_cutoff":
>
> {* cutoff distance in Angstroms for identification of breaks *}
> {* the default of 2.5A should be reasonable for most cases. If the input
> structure has bad geometry it may be necessary to increase this
> distance *}
> {===>} break_cutoff=2.5;
>
> You may also try switching off the automatic detection of mainchain breaks:
>
> * automatically detect mainchain breaks in proteins based on distance *}
> {* the peptide link at break points will be removed *}
> {+ choice: true false +}
> {===>} auto_break=true;
>
> It is also worth checking that the offending residues have their full
> complement of backbone atoms in appropriate places (not accidentally
> zapped to far-flung regions of coordinate space).
>
> Cheers,
> James

Hi James,

I tried to increase the parameter value to 3.0 A. The resulting file gives
the same behaviour (and the newly introduced OXTs are within 0.05 A of the
N atom of the following residue) so I think the distances are reasonable.

So unfortunately I think your valuable suggestion does not solve the
problem. On the graphics with Coot the starting model looks fine in these
regions.

I need to keep the automatic mainchain break detection because there are
some gaps in each chain of the model (12 chains in all).

So if there are other suggestions to solve this b....r of a problem, they
are most welcome!

Fred.

--

Fred. Vellieux, esq.

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CCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007

Previous message:
Subject: Re: CNS v1.2 and unwanted introduction of OXT
From: James Irving irving {- dot -} james {- at -} GMAIL {- dot -} COM
Date: 2007-03-05

Next message:
Subject: Re: Problems in MR
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-05