headers
David Langelaan | 15 Apr 2012 14:18
Picon
Picon
Favicon

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
Permalink | Reply |
headers
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
(Continue reading)

Permalink | Reply |

Gmane