hello imp users,
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 ?
I tried using it regardless, but it asks for a representation. I'm not sure how to get the representation. I tried the system, state, model, molecule, root_hierarchy, molecule.get_represented() ... how do i get the representation ?
any help greatly appreciated, thanks !
Josh
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
> 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. >
I would strongly advise against using saxs shapes to do fitting. The 3D shapes are highly degenerate. Use the PMI saxs restraint and find the correct weight (adjusting it over the course of the simulation if necessary), or resort to filtering if you cannot do otherwise.
Yannick
I could only find SAXSISDRestraint in pmi
I recommend to use saxs::RadiusOfGyrationRestraint as it is very fast. This will direct the model to the correct Rg and help to fit the low q portion of the profile. You can also calculate SAXS profile and score (chi) every X steps using saxs::Restraint.
If you use it with pmi, you will need to wrap these restraints into pmi restraints with python. Look at some other pmi restraints for example.
On Tue, Nov 29, 2016 at 11:41 AM, Yannick G. Spill yannick.spill@gmail.com wrote:
> > > 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. >> >> > I would strongly advise against using saxs shapes to do fitting. The 3D > shapes are highly degenerate. Use the PMI saxs restraint and find the > correct weight (adjusting it over the course of the simulation if > necessary), or resort to filtering if you cannot do otherwise. > > Yannick > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >
participants (4)
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Ben Webb -
Dina Schneidman -
Josh Bullock -
Yannick G. Spill