Hello Santhosh--
>
> From the example gb1_rdc [from the tutorial]. I see that model.pdb has?
> ATOM ? ?856 ?X ? ANI ? 500 ? ? 322.383 -47.025 154.522 ?1.00 ?3.06 ? ? ? ? ?
> ATOM ? ?857 ?Y ? ANI ? 500 ? ? 322.080 -50.957 156.088 ?1.00 ?4.37 ? ? ? ? ?
> ATOM ? ?858 ?Z ? ANI ? 500 ? ? 323.128 -50.368 152.019 ?1.00 ?4.35 ? ? ? ? ?
> ATOM ? ?859 ?OO ?ANI ? 500 ? ? 324.205 -49.405 154.647 ?1.00 ?4.04 ? ? ? ? ?
Those coordinates are cruft written long ago, and the Python scripts
do not actually read these.
>
> These 4 should define the tensor axis. And the RDC definition is done :
> assign ( resid 500 ?and name OO ?)
> ? ? ? ?( resid 500 ?and name Z ? )
> ? ? ? ?( resid 500 ?and name X ? )
> ? ? ? ?( resid 500 ?and name Y ? )
> ? ? ? ?( resid 2 ? ?and name N ? )
> ? ? ? ?( resid 2 ? ?and name HN ?) ?-3.7330 ?0.2000
In the Python interface, the first four atom selections are actually
ignored, and the alignment tensor is specified separately, and usually
you need not be concerned with the pseudo atoms. The table format remains
the same as that read by the old XPLOR RDC terms (dipo and sani) for
backward compatibility.
> And about the perpendicularity :
> Do you mean that I need not manually maintain perpendicularity in the
> model.pdb?
Like I said the pseudo atom coordinates are not read in, and
axis-orthogonality is maintained by the IVM in the Python scripts.
I hope this clears things up a bit.
Charles
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Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
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