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
