I think this was done by the default refine.py script. Or?
On Oct 26, 2016, at 10:26 PM, Clore, Marius (NIH/NIDDK) [E] wrote: > The other thing you need to do if you're going to fit NH RDCs together with > X-ray data is make sure you're in torsion angle dynamics mode so that the > covalent geometry is fixed. Otherwise you can always move the proton of the > NH bond to fit the RDCs perfectly and of course this will have absolutely no > impact on the agreement with the X-ray data as the X-ray scattering doesn't > see protons. > > > ------------------------------- > G. Marius Clore, MD, PhD > NIH Distinguished Investigator > Chief, Protein NMR Section > Laboratory of Chemical Physics > Bldg 5, Room B1-30I > NIDDK, National Institutes of Health > Bethesda, MD 20892-0520 > Tel: (301) 496 0782 > Fax: (301) 496 0825 > e-mail: [email protected] > web: http://spin.niddk.nih.gov/clore (Clore lab homepage) > http://www.nasonline.org/member-directory/members/20033168.html > (National Academy of Sciences web page) > http://www.ae-info.org/ae/User/Clore_G._Marius (Academia Europaea web > page) > ________________________________________ > From: Gabriel Cornilescu [[email protected]] > Sent: Wednesday, October 26, 2016 3:39 PM > To: Emmanouilidis, Leonidas > Cc: [email protected] > Subject: Re: [Xplor-nih] refine.py script handling off RDCs > > Hi Leonidas, > over fitted > I think the refinement worked fine, it's just indeed overfitted single > set of NH RDCs. It's easy to get the gb1 backbone to fit a single set of > NH RDCs by small torsion angle changes (see attached plot > refine_0_vs_start_model.png). You can see how the backbone was locally > deformed at residue Glu-15 to fit the RDC you changed from -9 to +5 Hz. > > If you fit the original set of RDCs to one of the structures you > calculated, you'll see that xplor fitted very well the original RDCs and > that the ones you altered are large outliers: > calcTensor -aveType sum -normType none -plot -showRDCs > tmv107_nh_orig.tbl refine_0.sa > (see attached refine_0_fit_orig_rdc.png) > > Adding the bicelle NH RDCs (attached as gb1_two_media.tar.gz) will > substantially reduce over fitting either set (rmsds are around 0.8-1.0 Hz): > calcTensor -aveType sum -normType none -plot -showRDCs tmv107_nh.tbl > refine_0.sa > (refine_0_with_bicelle_rdc.png attached). Again Lys-31 (with RDC changed > from +8 to -8Hz) stands out as an outlier. > > > The weight of the RDCs was high in that example to enforce agreement > with lots of RDCs in two media (including lots of small long-range ones, > with larger exp. errors). > > When using a single set in a single medium you therefore need to reduce > the weight of the RDCs until the scatter in the calculated structures > matches the experimental errors, i.e. change: > rampedParams.append( MultRamp(0.05,5.0, "rdcs.setScale( VALUE )") ) > > to something like: > rampedParams.append( MultRamp(0.05,0.2, "rdcs.setScale( VALUE )") ) > > So basically you can fit efficiently your X-ray structure to a set of > RDCs (but make sure you don't over-fit it). If you have independent sets > of RDCs you can use them initially to cross validate your results and > later include them all in the refinement. > > Hope it makes sense, > Gabriel > > On 10/26/2016 09:16 AM, Emmanouilidis, Leonidas wrote: >> Dear Dr Cornilescu, >> >> please find attached the folder as you asked. If you need anythin else >> please let me know. >> >> kind regards, >> Leonidas Emmanouilidis >> >> >> >> ________________________________________ >> From: Gabriel Cornilescu <[email protected]> on behalf of Gabriel >> Cornilescu <[email protected]> >> Sent: Tuesday, October 25, 2016 8:53 PM >> To: Emmanouilidis, Leonidas >> Cc: [email protected]; Charles Schwieters >> Subject: Re: [Xplor-nih] refine.py script handling off RDCs >> >> If you can tar and zip the folder containing your test (except the huge >> xplor output file) and email it to me I will take a look. >> >> >> On 10/25/16 10:24 AM, Emmanouilidis, Leonidas wrote: >>> 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 >>> >> -- >> >> Thanks, >> Gabriel >> >> https://sites.google.com/a/wisc.edu/gabrielc/ >> > > _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
