Hello Krishna-- > Please find the attached wrefine.py script and the PDB-extract file for > coordinates. > > The file containing valiation issues (copied from PDB deposition website) is > also > included here. >
I see that the validation report isn't particularly clear. However, if you run the torsionReport helper program(*), you'll see that the omega angles contain significant deviations from 180 degrees. Looking at the wrefine script, I see that you are not using Xplor-NIH waterRefineTools.refine function, but rather some function that was added to your local version of Xplor-NIH, so I can't help too much more unless you modify your script to use our tools. I believe you should get good results with either eginput/gb1_rdc/refine_eefx.py or eginput/gb1_rdc/wrefine.py from Xplor-NIH version 2.45. best regards-- Charles * torsionReport will not work with the mmCIF file you sent me- a fix is required, and will be available in the Xplor-NIH release. However, torsionReport should work fine with the PDB files output from the Xplor-NIH scripts. _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
