Thanks for your response Dr. Schwieters. I'm running my restraints
through the calcTensor.py script, however getRDCType is having problems
picking up my methyl groups (THR methyl groups specifically). I was
just going to add the following command to getRDCType:
if re.search(r"CBCG2",cName):
return 'CH'
would you expect this to cause any problems?
Thanks,
Andrew
Charles at Schwieters.org wrote:
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> Hello Andrew--
>
>
>> I am using RDCs to refine an nmr structure and I want to make sure
>> I'm setting things up correctly. I have 1 bond CH and NH RDCs from the
>> same sample in the same alignment medium with the same measurement error.
>>
>> 1)RDCs for methyl groups were multiplied by a factor of -3 to compensate
>> for the effects of rotation, and the angle defined along the C-C bond.
>> (A bit of confusion here, some sources say multiply by -3, and some say
>> divide. Also, if I'm defining the methyl CH RDC using the C-C bond, do
>> I need to rescale the data relative to CC, and then again to NH?)
>>
>
> start with eginput/gb1_rdc/anneal.py. The comments in the script walk
> you through this. Easiest is to leave the rdcs unscaled and uncomment
> the scale_toHN line.
>
>
>>
>> 2)I scaled (by hand) the CH RDCs to NH by multiplying them by a factor
>> of about -1/2, using values for gyromagnetic ratios and bond lengths
>> from rdcPotTools.py, and the fact that the gyromagnetic ratio is
>> negative for Nitrogen and positive for Carbon.
>>
>
> - From the comment at the top of python/rdcPotTools.py:
>
> protein residual dipolars are usually normalized relative to
> measurements of N-HN - this is achieved by calling the function
> scale_toNH. This normalization involves the gamma_A * gamma_B /
> rAB^3 prefactor (see the docs for <m rdcPot>). 15N has a negative
> gyromagnetic ration, but it was deemed simpler to treat as positive,
> so that if there is an experiment which doesn't include 15N, the
> dipolar coupling sign must be flipped. If you would rather not use
> this convention, call the function correctGyromagneticSigns() at the
> beginning of your script, and then the correct signs will be used
> for the Da prefactors.
>
>
>
>> 3)I used gridsearch.inp to find two sets of Da and rhom values, one set
>> for the scaled CH data, and one for the NH data. (If I have to rescale
>> the methyl CH RDCs to CC, do I need a third set of Da and rhom
>> values?)
>>
>
> If you have structures you should use
> eginput/protG/calcTensor.py
>
> This is faster and more accurate than a gridsearch, and allows you to
> easily incorporate all of your rdcs.
>
>
>> 4)Force constants for CH were multiplied by about 2 relative to NH (the
>> inverse of the scaling factor used in step 2)
>>
>>
>
> Again, see gb1_rdc/anneal.py.
>
> best regards--
> Charles
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