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
-- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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