Dear Charles,
I did as you told me:
> You need to call correctGyromagneticSigns before the calls to
> create_RDCPot. i.e.
>
> from rdcPotTools import create_RDCPot, scale_toNH, correctGyromagneticSigns
> correctGyromagneticSigns()
> rdcs = PotList('rdc')
> for (medium,expt,file, scale) in \
> [('p','NH' ,'gyrNH_20110823.tbl' ,1),
> ('p','NCO' ,'gyrNCO_20110823.tbl' ,4.0),
> ('p','CACO' ,'gyrCAC_20110822.tbl' ,10.0)
> ]:
> rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
> rdc.setPotType('square')
> scale_toNH(rdc)
> rdc.setScale(scale)
> rdc.setShowAllRestraints(1) #all restraints are printed during analysis
> rdc.setThreshold(1.0) # in Hz
> rdcs.append(rdc)
> pass
> potList.append(rdcs)
> rampedParams.append( MultRamp(0.00005,2.8, "rdcs.setScale( VALUE )") )
>
> hope this fixes things--
> Charles
>
well it fixed things, more or less. I mean, when I use the
correctGyromagneticSigns() function in the position you suggested me I find
a relevant decrease of the overall energy, and in particular of the angular
and improper energy terms.
I rather think I've misinterpreted the following statements:
"15N has a negative gyromagnetic ratio, 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."
So, as far as I understand I should calculate my RDCs as
A) Nitrogen (NH & NCO): |J+D| - |J|
B) non-Nitrogen (CACO): |J| - |J+D|
"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"
So, using this function XPLOR-NIH changes everything to the "natural" sign:
A) Nitrogen (NH & NCO): |J| - |J+D|
B) non-Nitrogen (CACO): |J+D| - |J|
is it correct?
I still wonder why if I use the RDCs calculated with their "natural" signs
and avoiding the use of correctGyromagneticSigns (and keeping the same
alignment tensors parameters and force constants), I obtain a far higher
energy and different Euler angles.
Said so, in the meanwhile I'll keep on working with the correcting function
activated and RDCs with "flipped" signs as suggested by Xplor NIH online
documentation.
Best regards,
Carlo
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