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Hi-- > I have been attempting to utilize the xplor-nih package for structure > calculation using static chemical shift and dipolar coupling data. (For > now 15N-1H) Unfortunately, the implementation of the 15N CSA seems to be a > bit problematic. I had hoped that the previous tensor definitions used > fitting the residual 15N CSA would be close enough for a start and > require only adjustment of the scaling factor. I have been using a small > helical test system oriented in xplor by fitting to the dipolar couplings, > whose 15N chemical shifts have been simulated using validated scripts in > matlab. Atom selection for the 15N CSA is identical to Dr. Tjandra?s > Practice Manual, and currently a 0.001 scaling factor, da=1, and rhomb=0 > are being used. The calculated Xplor CSA values are significantly > different from the observed values (matlab), and give a figure-8 pattern > when correlated to the dipolar coupling (rather than the distinct > wheel-like pattern from the observed). Varying the order of the sigma > components does not approach a scalable difference between the xplor and > observed results. Results are sensitive to atom selection and tensor > type, which I believe is a good sign. Hard to say what's going on here. You might send me a tarred-up set of script+support files, and I could take a look. I also might run things by Nico to see if he spots a problem. > > I have noticed in the current distribution (2.9.9) that the nitrogen > tensor is not included in the csaPotTools and flagged as not being > supported; however, the nitrogen type does appear to be identified (since > the definition does not default to the 31P values). These can be added easily- I had wanted to wait until I had an example with an XPLOR script, so I could verify the results. You might add the missing entry, if you have the values- or I might do this if we can get your XPLOR script working properly. > > I have also attempted to use the csaPotTest included with the binary to > check the distributions we are currently running. I would have assumed > that the test script would have been to verify the xplor calculated values > were the same as the input values; however, on both Darwin and Linux > distributions , I am seeing identical outputs showing significant > differences between the xplor calculated and the input csa. > actually, this is not a problem- the calculation just acts as a check that the numbers don't change after we've validated the results. Proper refinement is not performed in the tests, so good agreement between calculated and observed results are not expected. Having written that, the test will be modified a bit for the next release... regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.5 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFCRY09PK2zrJwS/lYRAuo+AJwNQla6VUwWXoZ1gm5TRNYId0zkvACeP1F1 mGNmV3YyM8G1pwPgTb15b6s= =TIxV -----END PGP SIGNATURE-----
