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[ccp4bb] NAp dictionary files attached for NAD and FAD
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: NAp dictionary
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
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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

I'm using cif files for NAD and FAD that I made with phenix.elbow. I had to
lower the planar esds for a few atoms to ensure planarity of the adenine
rings (grep for jt in the attached cif files). They work fine in coot and
phenix.refine. Riboses are not planar; aromatic ring systems are planar. I
have not tested them in refmac.


On 7/1/08 9:31 AM, "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
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>
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