Hi xplorers, I am trying to use different sets of RDCs and was a bit confused by the scaling function scale_toNH().
I am wondering whether the NH means amide N-HN or nucleic acid N-H group. In the rdcPotTools.py it says: scale_toNH(rdc,type=0): scales the given expression for dipolar coupling such that given Da=scale*Da_NHN But the expression to calculate scale states: scale = Da_prefactor[type] / Da_prefactor["NH"] while Da_prefactor["NH"] = gamma_N * gamma_H / r_nh**3 r_nh = r_caha / (gamma_C/gamma_N*0.48125)**(1./3) Quite interestingly, given the r_caha, gamma_C, gamma_N values in the rdcPotTools.py, I get r_nh=0.647731, while r_nhn is 1.042 in the same file. So if I scale amide N-HN couplings, I do not get a scale factor of 1? And I also notice Da_prefactor["HP"] = gamma_H * gamma_P Da_prefactor["HH"] = gamma_H * gamma_H Does this mean r_HH, r_HP are set to 1? And does anyone have the canonical bond distance for Ca & Cb? It would be good to add type CACB in rdcPotTools.py. I found the r_?? used to calculate scale factors are different from those in the protein.par, thus I am not clear which value should I use for scaling. I am using xplor-nih v2.14 Atom __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
