Any official conclusion on this RDC data / Cartesian minimization issue?  Is
it best for those of us using RDC data to skip that final Cartesian space
minimization? Or maybe to perform it but without the RDC potential?

Thanks!

Lisa Tuttle
Klevit Lab 
University of Washington

-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Gabriel Cornilescu
Sent: Wednesday, October 26, 2016 6:23 PM
To: Clore, Marius (NIH/NIDDK) [E] <[email protected]>;
Emmanouilidis, Leonidas <[email protected]>
Cc: [email protected]
Subject: Re: [Xplor-nih] refine.py script handling off RDCs

Marius, there's indeed a final minimization in cartesian space (minc) in the
end of the script. I'll comment it out and run the test again, curious how
different the result will become when everything will be minimized in
torsion space exclusively.


On 10/26/16 8:10 PM, Clore, Marius (NIH/NIDDK) [E] wrote:
> Leonidas and Gabriel,
>
> I'm out of town right now and so don't have access to the script.
However, if my memory serves me right you will find that the script contains
a final minimization step in catesian space (you can check this yourself or
ask Charles).  In any case, the consequence of that is that you'll always
get perfect agreement with the NH RDCs because all one has to do is move the
protons around a bit and there is no constraint from one proton to the next
(i.e. each proton would be moving independently of the others).  Even if you
had multiple media you really wouldn't be doing anything except moving the
protons around (of course the agreement then wouldn't be perfect as there
would be discrepancies between the different media) and there would be
absolutely no interaction with the X-ray data.
>
> Now, if you had measured NC' or CaC' RDCs, i.e. backbone which is impacted
by the X-ray data you would find that the X-ray data would always dominate
and there would be minimal improvement in agreement with the RDCs and
minimal shifts in the backbone coordinates.
>
> Marius
>
> ________________________________________
> From: Gabriel Cornilescu [[email protected]] on behalf of Gabriel 
> Cornilescu [[email protected]]
> Sent: Wednesday, October 26, 2016 8:43 PM
> To: Emmanouilidis, Leonidas
> Cc: Clore, Marius (NIH/NIDDK) [E]; [email protected]
> Subject: Re: [Xplor-nih] refine.py script handling off RDCs
>
> Yes, the refine.py script in the eginput/gb1_rdc uses torsion angle 
> dynamics. The script has a comment section about expt. error scaling.
> This is mentioned in the xplor-nih documentation as well. Moreover, 
> most papers and reviews on structural refinement using RDCs discuss 
> this important issue in more detail.
>
> E.g. see:
>
> see min. 44 of:
> https://www.youtube.com/watch?v=bmx56Fjv8Hc
>
> and
> https://spin.niddk.nih.gov/clore/Pub/pdf/325.pdf
>
>
>
> On 10/26/16 6:42 PM, Emmanouilidis, Leonidas wrote:
>> 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/
>>>>
> --
>
> Thanks,
> Gabriel
>
> https://sites.google.com/a/wisc.edu/gabrielc/
>

-- 

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

_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih

Reply via email to