Thanks for the response, and sorry for the confusion.
One final questions. After running refine.py, the orientational tensor
atoms end up sitting right on top of my peptide. Can I assume that no
interactions are calculated between the tensor atoms and anything else?
Andrew
{Sorry for the accidental direct email Dr. Schwieters}
Charles at Schwieters.org wrote:
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> Hello Andrew--
>
>
>> When determining Da and Rhom, is it acceptable to lump all the (scaled)
>> data into one file and determine a single Da and Rhom for the whole lot?
>>
>> The convention in the literature seems to be to determine Da and Rhom
>> for one data set and the estimate Da for all other data sets by scaling
>> the calculated Da by the appropriate gyro_mag/bond length ratios. The
>> current Xplor_NIH convention seems to be to scale all data to NH and
>> then choose a single Da and rhom for all data sets that is close to the
>> Da and rhom values for the individual scaled data sets. I'm a little
>> leery of these using either of these conventions because I have few data
>> points (21 CH and 10 NH), and if I run the scaled individual data sets
>> through SVD I get fairly different values for da and rhom between the
>> two data sets (14.04/.093 for scaled CH and 8.86/.057 for NH). {For
>> comparison, I ran the individual data sets in eginput/gb1_rdc through
>> SVD and got very similar Da and rhom values} My thought was then to lump
>> the scaled data together since, in general, more data points = more
>> accurate results. Is this a fair assumption? Are there better ways I
>> could go about this?
>>
>>
>
> I'm not certain what you mean by your question. Whatever method you use,
> all observed rdcs should be used to determine the Da and Rh. If you have
> pre-calculated structures, eginput/protG/calcTensor.py does this using
> SVD. If you have no structures, use calcDaRh and use that as a starting
> point for eginput/gb1_rdc/anneal.py, followed by refine.py. anneal.py
> fixes Da/Rh until final minimization. refine.py allows Da/Rh to float
> throughout. In all cases, all available data should be used (from all
> experiments).
>
> best regards--
> Charles
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