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Hello Jeff--
>
> I tried to use addAtoms.py with XplorNIH 2.19 to add 11 MTSL groups to a 183
> residue protein and got the following:
>
>
> 1. Is there something other than what I did above that can be tried to get
> correct geometry when using addAtoms.py with XplorNIH 2.19?
that is the correct procedure. Did you use the parameters in
eginput/PSF_generation/cysp.par? These should work fine. Where were the
violations (these should be reported)?
> 2. Is there any way to get pdb and psf file output from addAtoms.py with
> XplorNIH 2.19 instead of an error message even if the geometry is not
> correct?
yes. replace the lines
protocol.addUnknownAtoms(dyn_stepsize=0.01)
protocol.fixupCovalentGeom(sel=notKnown)
with
import protocol
try:
protocol.addUnknownAtoms(dyn_stepsize=0.01)
protocol.fixupCovalentGeom(sel=notKnown)
except protocol.CovalentViolation:
pass
> 3. Is there a way to make the addAtoms.py geometry correction more
> robust? If yes, what is the best approach?
This is an ongoing project of mine. It would be helpful if you upload your
failing case to
ftp://nmr.cit.nih.gov/pub/schwitrs/incoming/
so that I can fix it in future versions. Also, please tell me which
platform you're running on.
thanks and best regards--
Charles
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