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: MTZ to Shel-X?
From: "Ian J {- dot -} Tickle" i {- dot -} tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-03-05

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

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

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

CCP4bb navigation

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

Previous message:
Subject: Re: MTZ to Shel-X?
From: "Ian J {- dot -} Tickle" i {- dot -} tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-03-05

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