Hello Yikan--
>
> Now I am doing an ensemble simulation, the simulation is restrained just by
> the
> SAXS data, and the starting structure is predicted by rosetta. the script is
> just
> like below:
>
> xplor.requireVersion("2.19")
>
> import protocol
> protocol.initRandomSeed()
> protocol.topology['nucleic']="nucleic-2.0.top"
> protocol.parameters['nucleic']="nucleic-2.0.par"
> protocol.initParams("nucleic")
>
> xray_scale = 400
>
> numberOfStructures=100
>
> fn_pdb = "tbox_0612.pdb"
> fn_saxsData='sEC_30.dat'
>
> ensembleSize = 1
> #by default, all ensemble members have equal weights, but you can change this:
> #
> ensWeights=[1.0/ensembleSize for i in range(ensembleSize)]
> ####ensWeights=[0.8,0.1,0.1]
>
> startStructure=0
> outFilename = "SCRIPT_%d_STRUCTURE_MEMBER.pdb" % numberOfStructures
>
> rigidRegions=[
> 'resid 1:16 or resid 92:104',
> 'resid 25:82',
> 'resid 118:137',
> 'resid 142:174',
> 'resid 186:235',
> ]
> breakResids=[91,24,117,141,185,]
> ………..
>
> I want to know: 1) what is the relationship between “numberOfStructures” and
> “ensembleSize”?
numberOfStructures is the number of ensembles to calculate.
ensembleSize is the size of each ensemble
> 2)Does the “numberOfStructures” will affect the chi^2 results?
Only in the sense that if you calculate more ensembles, there is a
better chance to converge to a better answer.
> 3) how does "xray_scale = 400” affect the process of simulation? if
> I just want to do ensemble simulation against the SAXS data, the
> higher value of “xray_scale” will be better (for example 4000)?
as always, the force constant should be set to get the best possible
fit for that energy term (SAXS chi^2 in this case), while not
affecting the other terms (probably mostly nonbonded and torsionDB in
this case) too adversely.
best regards--
Charles
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