Hi, I am so far using a distance restraint, which is satisfy if the particules are below the distance, down to 0, ie contact. Is that correct? Then what is the point of the std_dev if it is anything below distance that score lowest?
So far, my code is something like
<Distance> <Restraint name="mydist" distance="10" std_dev="1"> <Particle id="prt1"/> <Particle id="prt2"/> </Restraint> </Distance>
However, I would like to have a function with a minimal score if the particules are at the give distance, with some stdev. I probably need to use the DistancePairScore function. But how to do that in XML format?
Thanks for IMP and the support
**************** Damien Devos Center of Organismal Studies Ruprecht-Karls-Universitat Im Neuenheimer Feld 230 69120 Heidelberg, Germany
On 06/30/2012 10:06 AM, damien.devos@cos.uni-heidelberg.de wrote: > I am so far using a distance restraint, which is satisfy if the > particules are below the distance, down to 0, ie contact. Is that > correct? Then what is the point of the std_dev if it is anything below > distance that score lowest?
No, this is a harmonic distance restraint. It keeps the distance to 10 angstroms with a standard deviation of 1.
> However, I would like to have a function with a minimal score if the > particules are at the give distance, with some stdev. I probably need to > use the DistancePairScore function. But how to do that in XML format?
Restrainer only supports a subset of IMP restraints, and it is designed to work with experimental types (e.g. "pulldown" or "yeast 2-hybrid") rather than mathematical forms (e.g. "harmonic"). If you want more flexibility, you'll have to write Python scripts instead. That said, restrainer's distance restraint should do exactly what you want here.
Ben
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damien.devos＠cos.uni-heidelberg.de