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
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--
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/
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