hello all,
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”? 2)Does the “numberOfStructures” will affect the chi^2 results?
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)? Thank you!
Best,
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
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