Dear Jacob:
Your syntax does not not appear to be quite correct. You need nested
parenthesis for the "ambiguous" atom in ambiguous restraints restraints.
The following is an example between a compound proton H9 (unambiguous)
and three possible methyl groups on the protein. Segment identifiers are
used to distinguish compound and protein. You need to specify the bounds
at the end of the assign statement:
assign (segid CMPD and resid 1 and name H9) ((segid PROT and resid 70
and name HD*)
or (segid PROT and resid 92 and name HD*) or (segid PROT and resid
107 and name HD*)) 1.8 0.0 2.2
You may also want to explicitely set averaging=sum.
Kieth
Jakob Toudahl Nielsen wrote:
>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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