Dear all,
I am testing a refinement protocol using ambiguous distance restraints
editing the "~/eginput/gb1_rdc/refine.py" xplor-nih python script
template.
Most of my ambigous distance restraints contain the OR syntax (here
ambiguous hydrogen bonds):
-------------------------------
assign (resid 14 and name O) (resid 2 and name HN) 1.00 1.00 1.00 OR
(resid 15 and name HN) (resid 2 and name O) OR
(resid 14 and name O) (resid 3 and name HN) OR
(resid 15 and name HN) (resid 3 and name O) OR
...
...
-------------------------------
The files pdbTemplatename.viols and averageFilename.viols reports much
violations that expected. I use the xray-structure as starting
structure which should have only 10 violation but end up with 48
violations after refinement. Inspection of the .viol files reveals
that the violations are exclusively reported with respect to the first
sele pair in the ambioguous distance restraint. I.e. violation for the
distance between 14O and 2HN in the example above regardless if 15HN
and 3O fullfill the distance restraint.
I end up with high noe violation energy (3689 with scale 30 and soft
with asympSlope=0.2)
I do not specify the setAvetype("sum") - this is the default - right?
I only observe very few violations for the unambiguous distance restraints
It seems like either:
1) I am missing something obvious - sorry if this is the case!
2) The analyze procedure does not recognize the OR syntax.
3) The OR syntax is not recognized at any stage.
What do you think is the problem?
Any help wpuld be very much appreciated!
Best regards,
Jakob
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