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. > > > We rerun the refinement protocol using xplor version 2.45. But still getting > covalent geometry violations. Please find the attached stats file generated > during this run. >
I want to confirm that your script is now using waterRefineTools.refine for structure calculation. Assuming you are, I'll address the results in your .stats file. First the DIHE violations can be ignored for now- the default threshold value for that term is much too small (2 degrees). You might try fixing that up by adding this line to the top of your script: import xplorPotTools xplorPotTools.defaultThresholds['CDIH'] = 25 The angle, improper and VDW violations are more worrisome. What kind of results do you get from refine.py? You might run that first because it uses a much simpler force field. If that script results in these sorts of error, there is likely a direct conflict between your experimental restraints and the force field- and that should be understood. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
