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:[log in to unmask]
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