Hello Kent--
>
> 1. Is there a way to have a square-well coordinate restraint?
>
> I am refining a structure against a layered CryoEM density, and I would like
> to have a way to keep one peptide from moving into the next layer. I see the
> possibility of Harmonic Coordinate Restraints, but do not see a square-well
> option (and also do not know how to implement the Harmonic Coordinate
> Restraint in Xplor-NIH).
Sure. Use a PosDiffPot, and set a nonzero upper bound:
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD","name CA C N O",
pdbFile='model.pdb',
cmpSel="not name H*")
refRMSD.setUpperBound(1.0)
The above will restrain the specified backbone atomic coordinates to
those in model.pdb, but give zero energy for RMS deviations under 1 Angstrom.
https://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/posDiffPotTools.html
>
> 2. How can I output the Atom Density map that results from the
> “probDistPot” optimization against the EM density?
>
> In the description of “probDistPot,” I see listed
> prStruct - atomDensity.AtomDensity object which contains the
> map computed from atomSel.
My apologies- that documentation has not be updated. It should read:
prStruct - atomProb.AtomProb object which contains the
map computed from atomSel.
And this object has the method writeEDM(filename), which will write an
XPLOR-EDM-formatted map. Also, I believe
prStruct.getGrid().writeCCP4(filename)
should get you a CCP4-formatted map.
best regards--
Charles
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