user queries for the Xplor-NIH biomolecular structure determination program

Marcel Jurk | 29 Mar 2012 15:31

Hello,

Hello,

I was trying to do an ensemble refinement of a dimeric structure and keep getting the following error
message. Is the NCS potential the only one that's not supported in ensemble mode or am I missing any kind of
additional function to call before the set-up of the NCS potential?

Best regards,
Marcel

Traceback (most recent call last):
  File "<string>", line 2, in <module>
  File "/opt/xplor-nih-2.30/python/trace.py", line 180, in run
    exec cmd in dict, dict
  File "<string>", line 1, in <module>
  File "gen_models.py", line 287, in <module>
    ncs1 = create_PosDiffPot("ncs1","segid A","segid B")
  File "/opt/xplor-nih-2.30/python/posDiffPotTools.py", line 93, in create_PosDiffPot
    pot.addEquivAtomPair( selection[i], selection2[i] )
  File "/opt/xplor-nih-2.30/python/wrappers/posSymmPot.py", line 159, in addEquivAtomPair
    def addEquivAtomPair(self, *args, **kwargs): return
_posSymmPot.PosSymmPot_addEquivAtomPair(self, *args, **kwargs)
SystemError: xplor-nih error: PosSymmPot::addEquivAtomPair: EnsembleSimulations are not supported

Marcel Jurk
Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
Solution NMR (AG Schmieder)
Robert-Roessle-Str. 10
13125 Berlin
Germany

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Charles Schwieters | 29 Mar 2012 17:44

Re: Hello,


Hello Marcel--
>
> I was trying to do an ensemble refinement of a dimeric structure and
> keep getting the following error message. Is the NCS potential the
> only one that's not supported in ensemble mode or am I missing any
> kind of additional function to call before the set-up of the NCS
> potential?

For symmetric dimers, usually two terms are used in single structure
calculations, an ``NCS'' term to force the subunits to be identical
and a distance symmetry term to enforce C2 symmetry. These terms can
be used in ensemble calculations to force each ensemble *member* to have
these properties, however this is over-restraining the system, as, in
general, only the overall ensemble requires these symmetries. In
the latest Xplor-NIH release, the distance symmetry term can be used
to restrain the average ensemble position using the setup below. There
currently is no term for the NCS portion- I happen to be working on it
now and hope to have something working by next week.

best regards--
Charles

from distSymmTools import create_DistSymmPot, genDimerRestraints
dSymmP = create_DistSymmPot('dSymmP')
for r in genDimerRestraints(segids=['A','B'],
		            #specify appropriate range
                            resids=range(10,150,10)):
    dSymmP.addRestraint(r)
    pass

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Marcel Jurk | 3 Apr 2012 14:23

Re: Symmetry and NCS Potentials in Ensemble Calculations

Thank you Charles for the kind explanation. I am already looking forward to your implementation of NCS
potentials in ensembles.

Best regards,
Marcel

Marcel Jurk
Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
Solution NMR (AG Schmieder)
Robert-Roessle-Str. 10
13125 Berlin
Germany

eMail: jurk <at> fmp-berlin.de
Phone: +49-30-94793223
Fax: +49-30-94793169

>>> Charles Schwieters <charles <at> schwieters.org> 03/29/12 5:44 PM >>>

Hello Marcel--
>
> I was trying to do an ensemble refinement of a dimeric structure and
> keep getting the following error message. Is the NCS potential the
> only one that's not supported in ensemble mode or am I missing any
> kind of additional function to call before the set-up of the NCS
> potential?

For symmetric dimers, usually two terms are used in single structure
calculations, an ``NCS'' term to force the subunits to be identical
and a distance symmetry term to enforce C2 symmetry. These terms can

(Continue reading)