thank you very much for the suggestion. I have tried as you suggested, having random RDC values for residues 16,29,31,39,48,53 of gb1. The result was the same. Converence with perfect correlation obs/calc without really violations.
________________________________________ From: [email protected] [[email protected]] on behalf of Gabriel Cornilescu [[email protected]] Sent: Monday, October 24, 2016 11:18 PM To: Emmanouilidis, Leonidas Cc: [email protected]; Charles Schwieters Subject: Re: [Xplor-nih] refine.py script handling off RDCs That doesn't tell much, it's equivalent to having a 6% larger alignment tensor and the fit has to be identical. Try to either scramble a few assignments or add/subtract a few Hertz from just a handful of RDCs to see a difference. On Oct 24, 2016 3:52 PM, "Emmanouilidis, Leonidas" <[email protected]<mailto:[email protected]>> wrote: by random I mean addition of 6Hz to all HN-N rdcs. On Oct 24, 2016, at 10:43 PM, Gabriel Cornilescu wrote: When you say random, are you scrambling the assignments, changing the RDC values randomly by 6%, or changing their associated errors? On Oct 24, 2016 3:30 PM, "Emmanouilidis, Leonidas" <[email protected]<mailto:[email protected]>> wrote: This is relative simple. If one runs the tutorial-based gb1 RDC refinement protocol (refine.py) but with hn RDCs values completely random (+6Hz noise to each), the outcome is a seemingly successful refinement with no errors. I did the test using just the hn RDCs. On Oct 24, 2016, at 10:11 PM, Charles Schwieters wrote: > > Hello Leonidas-- > >> >> while I am trying to refine a crystal structure with RDCs using the >> refine.py script, I came across a weird result. >> >> I had near perfect correlation between observed and calculated RDCs >> values, which was fishy. After addition of 5Hz systematic noise to all >> RDCs, i still had perfect correlation and nice convergence with no >> violations(!). Initially i thought that there was something wrong with >> my experimental setup (since i only used RDCs+dihedrals restrains), >> but I had exactly the same result when I changed also the gb1 tutorial >> RDCs values. >> So to sum it up, I used the tutorial script (refine.py) and input >> files for RDC refinement, regardless of how much I alter the RDCs >> values (i tried up to +6Hz noise addition) I get always nice >> convergence, perfect correlation obs/calc with no violations. >> >> Is this how it should be or do I miss/mess somthing? >> > > Not sure what's going on- we'll need more details. > > best regards-- > Charles _______________________________________________ Xplor-nih mailing list [email protected]<mailto:[email protected]> https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
