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Hello Hyun--
>
> First thanks for your reply.
> I tried your script, and Code 1 works. But it changed coordinates too much.
> So I tried to specify the regions to refine covalent geometry at Code 2. But
> I got error message as follows:
> "PyInterp::command: error executing: >execfile('fix_11.py')"
>
You might try this:
import protocol, regularize
protocol.loadPDB('AAApdb')
protocol.addUnknownAtoms('AAA.pdb')
try:
protocol.fixupCovalentGeom(useVDW=True,sel=AtomSel('(segid A and (resid 48 or
resid 66 or resid 176 or resid 184 or resid 256 or resid 48 or resid 63 or
resid 65 or resid 66 or resid 108 or resid 109 or resid 226 or resid 243 or
resid 244 or resid 333 or resid 334 or resid 365 or resid 366 or resid 372 or
resid 373 or resid 374)) or (segid B and (resid 459 or resid 461 or resid 503
or resid 579 or resid 698 or resid 766 or resid 767 or resid 400 or resid 401
or resid 448 or resid 458 or resid 459 or resid 502 or resid 503 or resid 621
or resid 638 or resid 639 or resid 759 or resid 760 or resid 761 or resid 767
or resid 768))'), maxIters=1000)
except regularize.CovalentViolation:
pass
protocol.writePDB('BBB.pdb')
This should at least write out the structure. If the violations are
still too many, or too large, a more sophisticated fix-up procedure can
be used in which we allow atom positions to move, but not too much.
best regards--
Charles
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