Hi Keith--
>
> I am trying to refine a structure using NMR constraints. We have
> evidence that the molecule is a trimer held together by inter-chain
> disulphide linkages. The chains are synthetic, and we appear to have
> populations with different arrangements of the disulphide linkages -
> so I want to refine against an ensemble of possible structures that
> differ by their arrangement of disulphide bonds.
>
> I've looked at the scripts in ../eginput/dna_refi and
> ../eginput/gb3_ensemble, but they all appear to rely on generating
> the ensembles using dynamics to generate the different
> conformations. Is it possible to start the ensemble refinement using
> molecules that differ in their covalent bond ordering? If so how?
>
Yes. The closest example is in eginput/capsid. To set things up you do
startStructures=["file1.pdb",
"file2.pdb",
]
from ensembleSimulation import EnsembleSimulation
esim=EnsembleSimulation('ens',len(startStructures) )
ensIndex=esim.member().memberIndex()
protocol.loadPDB(startStructures[ensIndex])
For nonstandard proteins, you may need to use loadStruct/initCoords
with ensemble-member specific values for the PSF and PDB, instead of
loadPDB.
Please let me know if you have any problems with this.
best regards--
Charles
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