Re: [IMP-users] SAXSISDRestaint

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 <" target="_blank">> 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
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