Hi,
can you tell me how the energy value olde in the example script
http://salilab.org/modeller/manual/node264.html
(olde, dstate) = self.energy(state)
is calculated?
For an restraints file with N (physical.bond, physical.ca_distance, ...)
entries in it, how does the formula look like:
sum_i^N log(rsr_i), where rsr_i is defined as in
http://salilab.org/modeller/manual/node469.html? Are there any scaling
factors?
Best regards
Armin