Thanks for all the clarifications. I use the "export ARIA" button to
export my restraint sets.
>
>
>> 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).
Oh... I have just discovered that this is indeed no problem of the ARIA
export, but of the import of my Sparky data. Somehow, some of my Peaks
assigned to e.g. LEU-CD1-QD1 became LEU-CDa-HD*. I never did look this
closely on the import. I'll have to sort that out
>
>> 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.
>
Thank you for the hint. I never though of using the merits.
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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