Hi everyone,
Using Analysis in the refinement stage of structure calculations, I came
about some questions/issues/request around the generation and export.
The first one is a question about the "Distance function" in the
"Generate Distance Constraints" dialogue. Here you can select "NOE bins"
and "Normalized" but there is only one way do influence the setup (Set
distance classes). What is the difference between the two methods (I
cant't find it in the documentation)?
The second question is more about the handling of the restraints itself.
Although some restraints work on pseudoatoms (like methyl groups), this
fact seems not to be reflected in the distance that should be enlarged
to account for the difference between the geometric center of a group
(to which the restraint is applied) and the hydrogens. Another Issue is
the handling of non-stereospecificly assigned hydrogens which are
currently handled as ambiguous restraints. This allows independent
swapping for each peak/restraint loosing the connection of one resonance
to a single proton. In my understanding this should be handled during
structure calculation (by the lack of the stereo improper) that allows
the hydrogens or methyl groups to exchange their positions during the
high temperature phase of the simulated annealing retaining the
correspondence of one resonance to one proton.
My last point is more of a feature request. It would be nice, if one
could filter the peaks that are used for restraint generation in one or
the other way. Things one might want to exclude are intra-residue peaks
or ones that one "labelled" at some stage as "difficult" either due to
overlap or because they were close to the diagonal.
thanks,
Christoph
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Christoph Brockmann
Forschungsinstitut fuer Molekulare Pharmakologie (FMP)
Robert Roessle Str. 10
D-13125 BERLIN, Germany
phone: +49-30-94793-223
email: [log in to unmask]
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