Re: [ccp4bb] NAp dictionary

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

Previous message:
Subject: NAp dictionary
From: Jim Naismith naismith {- at -} ST-ANDREWS {- dot -} AC {- dot -} UK
Date: 2008-07-01

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Subject: NAp dictionary files attached for NAD and FAD
From: John Tanner tannerjj {- at -} MISSOURI {- dot -} EDU
Date: 2008-07-01

Subject: Re: NAp dictionary
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-07-01

It's odd because coot gives flat riboses even if you remove all the
torsion info from the dictionary
Phil

On 1 Jul 2008, at 15:31, Jim Naismith wrote:

> I don't know how many of you are frustrated with AO5* in NADP NAP
> (and in
> NAD). I trolled the web looking for a solution but did not find it.
>
> I think I have converted the current NAP nomenclature from the EBI
> in REFMAC
> and COOT to use the new agreed nomenclature for this residue. Simply
> replace
> your NAP.cif in the coot/share/lib/monomers/n/
> And in ccp4/lib/data/monomers/n/
>
> It is attached, along with a PDB file. This now works in both COOT
> and in
> REFMAC (as far as I can see). So now you can manipulate NADP in COOT
> without
> atoms getting left off or any kludges.
>
> There is still a problem with the dictionary in regularize COOT and
> REFMAC.
> It leads to a flat ring for the ribose. This is wrong, however, if
> in COOT I
> turn on torsion restraints goes haywire. This I think has always a
> been a
> problem with the original refmac dictionary.
>
> Anyway if anyone has a fix, please let me know.
> I suspect it is to do with periodicity of the torsion restraints. If
> I solve
> this I will email the BB.
>
> If anyone has done with this NAD, the community would benefit. Since
> I could
> not find the fix for NAP in my efforts.
>
> Best
> Jim
>
> James H. Naismith FRSE
Research mailto:naismith@st-
> and.ac.uk
> Professor of Chemical Biology
Teaching mailto:jhn@st-and.ac.uk
> Centre for Biomolecular Sciences
Office: 1334-463792
> The North Haugh
Fax : 1334-467229
> The University
Lab : 1334-467245
> St. Andrews
In UK add 0 to start of number
> Fife Scotland, U.K., KY16 9ST
http://www.st-and.ac.uk/~strucbio
>
> The University of St Andrews is a charity registered in Scotland : No
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>

CCP4bb navigation

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

Previous message:
Subject: NAp dictionary
From: Jim Naismith naismith {- at -} ST-ANDREWS {- dot -} AC {- dot -} UK
Date: 2008-07-01

Next message:
Subject: NAp dictionary files attached for NAD and FAD
From: John Tanner tannerjj {- at -} MISSOURI {- dot -} EDU
Date: 2008-07-01