Hello Jian-- > You are right, there are large violations. I'm confused about the > values that should be used in the CS and DC tables. Our > experimental collaborators have given us a table of the CS values > (let's call it Set 1), but another computational collaborator uses > the value that is subtracted by the isotropic value, 119.3 ppm for > non-Glycine residues (let's call this Set 2. In this table, each > value is the corresponding value from Set 1 minus 119.3). It seems > strange for me that when Set 1 was used, the structures look OK, but > with huge violations for CS; when Set 2 was used, the structure look > strange but violations are small. What do you think might be the > problem?
You might check out http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/csa-methods-marvin.pdf (referenced from) http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/csaPotTools.html > Do the simulation parameters in refine.py matter much? Is > there a script specifically designed for membrane proteins? please see eginput/assignFit/02refine.py in the Xplor-NIH distribution for an example. I hope this helps-- 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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