Hello Changdong-- > > As I only have PRE data for the protein/dna complex without any > intermolecular NOE constraints, the results from "newRefine.py" are not > good in which the input complex structure was modeled manually. > After searching the mailing list, Charles suggested in a message that > the calculation should be better started based on the > /eginput/diffTens/dock.py. > > I modified the dock.py and replaced the diffPot with prePot (the > chemical shift perturbation was not included). > > The script worked, but there two problems: > 1) the protein structures were disrupted in all the output > structures.
I suspect your ivm setup is incorrect. Please think carefully about the lines dyn_fix.group( 'resid 301:334' ) dyn_fix.fix( 'resid 94:207' ) dyn_free_sch.group( 'resid 301:334' ) dyn_free_sch.fix( 'resid 301:385 and (name CA or name C or name N or name O or name HN)' ) perhaps you intended to specify residues 94:207 in the final line? > 2) there is a relative orientation between protein and dna in the > output, but they do not have direct contact. > > I'm not sure the problem is coming from the experimental data or > something wrong in my modified script. > It would be best to use highly ambiguous restraints obtained from chemical shift perturbation analysis. Failing that, you might be able to use a Rgyr restraint to pull the subunits together. Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
