Hello Richard--
>
> I'm trying to include a cisProline in water refinement calculations -
> I'm
> using a modified version of the script found in
> eginput/gb1_rdc/wrefine.py.
> In earlier posts on this matter its suggested that there are two ways
> of
> doing this:
>
> 1) load a pre-generated PSF using protocol.initStruct, and then load
> the structure with protocol.initCoords instead of
> protocol.loadPDB.
This will not work unless, in generating your psf, you use the water
refinement topology files as specified in wrefine.py. A psf generated
using standard Xplor-NIH topology settings will not work with water
refinement.
>
> 2) load the structure with protocol.loadPDB, and then correct the PSF
> information using psfGen.cisPeptide.
>
> In the script I have:
> import psfGen
> protocol.loadPDB(inputStructures[0],deleteUnknownAtoms=True)
> psfGen.cisPeptide(110)
Unfortunately, the definition of the ``patch'' differs between
standard Xplor-NIH topologies and those used for water refinement. The
only way to do this on the fly here is to call the old XPLOR command
xplor.command('''
patch CIPP reference=nil=(resid XX)
''')
replacing XX with the appropriate residue number. psfGen.cisPeptide
should be fixed to give a more appropriate error message.
best regards--
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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