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Hello Hyun--
>
> I am new to XPLOR-NIH. After reading Xplor-NIH Documentation, I have one
> question.
> I built one pdb structure by homology modelling.
> When I checked the model structure by some programs, I found some warnings
> about unusal bond angle, chirality deviations. I want to fix them.
>
> Can I fix those warnings about bond angles, chirality by XPLOR-NIH
> refinement ?
Probably. The simplest thing to do is to try this simple script:
import protocol
protocol.loadPDB('in.pdb')
protocol.fixupCovalentGeom(useVDW=True)
protocol.writePDB('out.pdb')
In the likely event that this changes your coordinates too much,
something more sophisticated will be needed, and you will have to
specify which parts (and how much) to allow portions of your structure
to change.
best regards--
Charles
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