On Wed, 22 Feb 2006, Christoph Brockmann wrote:
> Using Analysis in the refinement stage of structure calculations, I came
> about some questions/issues/request around the generation and export.
How are you exporting the restraints - using the "export ARIA list" button
from the BrowseConstraints popup, or using formatConverter?
> 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)?
Tim can be definitive about this, but my take is that they are not
separate methods, but can be combined. Currently the analysis GUI
supports using distance bins (in the traditional strong, medium, weak,
very weak, or a more fine-grained approach at the user's control), but
there is also the possibility to apply a general intensity -> distance
mapping function (currently no GUI access). In the popup that allows you
to set your distance "bins" there is a column for the distances and
another for the intensity floor above which crosspeaks that have that
intensity should fall into that bin (unless they lie in a higher intensity
bin). Now, what are sensible numbers for these threshold values? ANSIG
(and maybe other software) typically used the normalised crosspeak
intensity (within a particular NOESY spectrum) for this mapping which in
practice allowed the same (or very similar) threshold values to be used
(at least for starting values) from project to project and spectrum to
spectrum when the NOESY is picked completely enough. This is the
behaviour that the normalise function reproduces. If you wish to set your
intensity thresholds based on the values for specific peaks in the NEOSY
spectrum, you might choose not to normalise and use values based on those
peaks.
> The second question is more about the handling of the restraints itself.
> Although some restraints work on pseudoatoms (like methyl groups), this fact
I can only agree with what Wim & Eiso have already written on this point.
Analysis does not currently write out pseudo-atom restraints (can't say
for formatConverter output) and a restraint to Ala HB* is not to a
pseudo-atom if treated as sum averaged in CNS/XPLOR.
> 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.
I have not observed any inappropriate behaviour for the case where
restraints are generated from the "export ARIA ..." buttons. Basically
the prochiral assignments (HBa, HBb, etc.) are mapped onto real atoms
(HB2, HB3, etc.) in the structure leaving your structure calculation
protocol to deal with the swapping (as the ARIA extensions to CNS/XPLOR
allow, and Eiso describes).
> 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.
This is essentially already there - set the peak merit value to some value
lower than 1 and use a minimum peak merit threshold.
Brian
--
Dr. Brian O. Smith ---------------------- B Smith at bio gla ac uk
Division of Biochemistry & Molecular Biology,
Institute Biomedical & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 8640
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