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Hi-- > 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. amide HN. I use scale_to_CH for nucleic acids. Sorry for the confusion- I need to add documentation to this effect. > > 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? > yes. NHN, Da_prefactor["NHN" ], and r_nhn are used for amides. the nh values are used for nucleic acids. You can see the individual values using the following scriptlet: import rdcPotTools print rdcPotTools.r_nh print rdcPotTools.r_nhn the values are slightly different. > 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? no. For experiments using these nuclei, you must turn on the variable distance feature- this is done for you by scale_toNH(). > > And does anyone have the canonical bond distance for Ca & Cb? It would > be good to add type CACB in rdcPotTools.py. I am accepting suggestions for this. > 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. > The distance value used in rdcPotTools has been corrected for vibrational motion. See JACS 120, 12334 (1998). hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFELE54PK2zrJwS/lYRAjxaAJ9OGKgM9c8U1GidFdsajkixViPhCQCeMHLl QYrv9KBK9xv9qGnnw4BdHpw= =UZDS -----END PGP SIGNATURE-----
