Hello Yikan--
>
> I want to generate a conformation pool for my RNA, so I used the
> EINemo to generate my perturbed structure. however, in my large
> bundle of pdb files from the EINemo, there are some violation in the
> geometry of bonds. Are there some useful tools(or tutorial) to fix
> my violation in the xplor-NIH?
If you have a an input PDB which you'd like to fix up while making
minimal changes, the following scriptlet may work. If it completes ok,
the output pdb should differ no more than 0.5 angstrom from the input
file, and it should contain no bond, angle or improper violations.
best regards--
Charles
import protocol
protocol.loadPDB('input.pdb',deleteUnknownAtoms=True)
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD","not name H*"
pdbFile=input.pdb')
refRMSD.setUpperBound(0.25)
refRMSD.setThreshold(0.25)
from regularize import fixupCovalentGeomIVM
fixupCovalentGeomIVM(extraTerms=[refRMSD],verbose=1)
protocol.writePDB('out.pdb')
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