On 11/28/16 3:21 AM, Josh Bullock wrote:
I'm trying to use the pmi.SAXSISDRestraint to model with crosslinks and SAXS, ideally all in the ISD ReplicaExchange method, however it says I need isd2. Does this exist anywhere, or is the SAXS restraint not working in this capacity ?
SAXSISDRestraint is an experimental Bayesian SAXS restraint. To the best of my knowledge it isn't ready for general consumption yet, hence its dependence on the experimental isd2 module (which also isn't released yet). Really not having isd2 should be a fatal error here.
PMI's SAXSRestraint should work though, although since it's non-Bayesian you may have to play with the weighting a little.
Note that since SAXS restraints are expensive to calculate, you may have better luck using SAXS as a filter on your final models, or perhaps generating ab initio SAXS shapes as input to the optimization.
Ben
--
https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle