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- Rgyr(potTerm)
- Vgyr(potTerm)
- analyze(potList)
- perform analysis of GyrPot terms and return nicely formatted
summary
- create_GyrPot(name, sel='not PSEUDO', targetVol=None, minResScaleFactor=12.28, maxResScaleFactor=18.66, softScale=0.0001, hardScale=1)
- create a gyrPot.GyrPot with the appropriate target volume for the
given atom selection
The relationship between number of residues and gyration ellipsoid volume
has been found to lie in the range minVol..maxVol, where
minVol = minResScaleFactor * numResidues
maxVol = maxResScaleFactor * numResidues
where numResidues is returned by selectTools.numResidues(sel).
This function creates two potential terms, soft and hard (whose
names have _s and _h suffixes, repsectively). The first has a target
value in the middle of minVol and maxVol. The second term has zero
energy in the whole range minVol to maxVol, but it has a much larger force
constant.
Alternately, if a non-None value of targetVol is specified, a single
energy term is included.
- create_RgyrPot(name, sel='not pseudo', targetRg=-1, rangeRg=0, gyrWeights=None)
- create a gyrPot.GyrPot configured as a radius of gyration restraint
with the specified target value of Rg. If rangeRg is positive, it is taken
as a +/- range about targetRg for which the energy is zero.
If targetRg is not specified it takes the value:
2.2 * Nres^{0.38} - 1
where Nres are the number of residues specified in sel.
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