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Marcel Jurk | 3 Apr 2012 14:23
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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
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Dr. Tatyana I. Igumenova | 5 Apr 2012 16:50
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dealing with flexible residues in RDC refinement

Dear Charles and others,

I am refining a structure of a protein that has several flexible residues (defined as residues for which
{1H}-15N NOEs are < 0.6).
I would like to make sure that I am taking this flexibility into account correctly during the RDC-driven refinement.

In brief, I have created two separate RDC potential classes, 'rdc_rig' and 'rdc_flx' and two separate
types of *.tbl files: one containing the "flexible" residues and the other containing the "rigid"
residues.  I then set the rdc_flx potential type to square:

rdc_flx.setPotType("square")
and left the default settings for the rdc_rig.

In the *.tbl files for "flexible" residues, I set the max error field to a large number (40 Hz) and the min
error value to 0 Hz for residues with positive RDCs, and min to 40 Hz and max to 0 Hz for residues with negative
RDCs.  Here is an example:

assign 
    ( resid 600 and name OO)
    ( resid 600 and name  Z)
    ( resid 600 and name  X)
    ( resid 600 and name  Y)
    ( resid   5 and name HA)
    ( resid   5 and name CA)     -3.6200  40.0 0.0 

assign 
    ( resid 600 and name OO)
    ( resid 600 and name  Z)
    ( resid 600 and name  X)
    ( resid 600 and name  Y)
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David Langelaan | 15 Apr 2012 14:18
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Duplicate restraint question

Hello,

Perhaps this is a silly question, but I have been looking around and 
could not find a satisfying answer anywhere.

If I give XPLOR-NIH several redundant distance restraints (same atoms 
and the same distance) does XPLOR keep only one of them or all of them. 
I am imagining that if XPLOR-NIH reads the same restraint multiple times 
(possibly due to diagonals or multiple types of experiments) then this 
restraint would be over-represented in the structure calculation leading 
to bias.

So my question is really two-fold:
1) Does XPLOR-NIH remove identical distance restraints from the energy 
calculation

2) If it doesn't, is this practically a problem and should I create a 
non-redundant distance restraint file as input to XPLOR-NIH?

Thanks!

David Langelaan
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Charles Schwieters | 16 Apr 2012 15:22

Re: Duplicate restraint question


Hello David--

>
> If I give XPLOR-NIH several redundant distance restraints (same atoms
> and the same distance) does XPLOR keep only one of them or all of them.
> I am imagining that if XPLOR-NIH reads the same restraint multiple times
> (possibly due to diagonals or multiple types of experiments) then this
> restraint would be over-represented in the structure calculation leading
> to bias.
>
> So my question is really two-fold:
> 1) Does XPLOR-NIH remove identical distance restraints from the energy
> calculation
>

no.

> 2) If it doesn't, is this practically a problem and should I create a
> non-redundant distance restraint file as input to XPLOR-NIH?
>

It's possible that this could cause a problem, particularly in
pathological cases. Note, however, that if the distance corresponds to
the zero-energy region of the potential term, the redudant terms will also
not contribute to the energy. If there are obvious redundancies I
would reove them.

best regards--
Charles
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