Hi guys, I've just started looking at the use of cross-validation for dipolar coupling refinement of protein structures in XPLOR-NIH. I can see how the R-factor is incorporated into an anneal script, and have all my couplings normalised to DNH, allowing me to report a working R(dip) for the total set. I would like to know whether there is an automated process for cross-validation? I'm assuming that I understand how to do it manually, that is:
* remove a reasonable percentage of couplings and re-calculate a working set of structures --> R-factor is generated for each structure by the anneal script and is R-work. * use only the couplings left out above and re-calculate a set of structures --> R-factor is generated for each structure as above but is now R-free. * do this for a few sets and compare the appropriate R-factors for cross-validation. Can this be done in the one script? I was thinking of joining 2 anneal scripts one after the other but I was interested to see if there is a more efficient way? Assuming I'm correct in my understanding of the cross-validation (I've read the JACS 121, 1999, paper a lot this weekend in between structure calculations and thesis writing and I think I've got it!), should I report R-factors as "factors" between 0 and 1, or as a percentage? I'm leaning toward the latter as a couple of recent publications report percentage, but I just want to make sure this is the standard way. Thanks in advance, Regards, Haydyn -- ---------------------------- Haydyn Mertens PhD student Dept. Biochem. University of Melbourne Australia
