[Xplor-nih] ambiguous distance restraint violations

[Jakob Toudahl Nielsen]

Dear Keith

I think my NOE table is setup correctly according to my intension: a  
set of individual atom pairs. I put the bound definition after the  
first assign pair

Quoting the manual:
"One or more optional OR clauses can be appended to the the ASSIgn  
statement, each introducing an additional ambiguous pair of selections  
to the given assignment. See Section 19.2.1 for an explanation of how  
these additional selections are used." (see  
http://nmr.cit.nih.gov/xplor-nih/xplorMan/node365.html#noe-ambiguity)

"A restraint created with the ASSIgn ... OR ... syntax has multiple  
pairs of atom selections, each of which is evalulated during the  
calculation of the average distance. When the ASSIgn ... OR syntax is  
used, SUM averaging is forced on, no matter which specifier is given  
to the AVERage statement"

I tryed my NOE table using a generic xplor protocol. This script runs  
with no errors (one 0-1 violations). Thus, I still hope for answers  
for my questions stated before... (see below)

Best regards,

Jakob

Citat af Keith L Constantine <keith.constantine at bms.com>:

> 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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