Hi Charles,
I tried different methods to calculate my protein. By xplor interface, I
tried sa.inp, dgsa.inp, and dg_full_embed.inp. I also tried the scripts for
python interface, like anneal.py.
The dgsa method gives the best result. However, for the scripts for python
interface, I haven't found the script including the dgsa method yet. Could
you please tell where I can find that script?
Another question is on the calculation including CSA. I have the anisotropy
values for amide N by using other simulation method.
The manual says the restraint list have the form:
assign (sel 00) (sel Z) (sel X) (sel Y)
(sel 1) (sel 2) (sel 3) obsShift error1 [error2]
My question is what atoms should be chosen for selection 1,2,3? Are the
observed chemical shifts the amide N chemical from spectra? How can I know
the error 1?
In xplor-nih, the chemical shift anisotropy is given by calcedShift =
sum_{i,j} A_i*sigma_j*cos(theta_(i,j))^2. So the anisotropy values I got
from other simulations are useless here, right?
Thanks a lot.
Best wishes
Si
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