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:[EMAIL PROTECTED]
and.ac.uk
Professor of Chemical Biology |Teaching mailto:[EMAIL PROTECTED]
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<NAP.cif><npx-coot-1_refmac1.pdb>
