[ccp4bb] NAp dictionary

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

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

Previous message:
Subject: faculty post
From: Issar Smith smithis {- at -} UMDNJ {- dot -} EDU
Date: 2008-07-01

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

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

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
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Fax : 1334-467229
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In UK add 0 to start of number
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CCP4bb navigation

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

Previous message:
Subject: faculty post
From: Issar Smith smithis {- at -} UMDNJ {- dot -} EDU
Date: 2008-07-01

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