Hi Celia,
I will add that for a detailed explanation of a standard Xplor-NIH script,
including the use of torsion angle restraints and their formatting, you could
check the reference below.
Guillermo
G.A. Bermejo and C.D. Schwieters, ``Protein Structure Elucidation
from NMR Data with the Program Xplor-NIH,'' Methods Mol Biol. 1688,
311-340 (2018).
________________________________
From: Woonghee Lee <[email protected]>
Sent: Friday, May 8, 2020 12:10 PM
To: List XPLOR-NIH <[email protected]>
Subject: Re: chemical shift restrain
Hi Celia,
I have waited Charles's response because he always brings something new to the
community that I might not catch up with well. If you are working on
NMRFAM-Sparky, you can try two-letter-code "c3" first that will automate NOESY
assignments, TALOS-N and Xplor-NIH calculation. You can customize the generated
Xplor-NIH scripts after the initial run.
Cheers,
Woonghee
On Fri, May 8, 2020 at 11:04 AM Charles Schwieters
<[email protected]<mailto:[email protected]>> wrote:
Hello Celia--
It seems that it took 3 days for your email to cross the Straights of
Florida. That's a pity.
> I am calculating the structure of a protein with Sparky. I already
> have NOE restrictions, but I also want to introduce proton chemical
> shift restrains.
When using Xplor-NIH, most commonly, or at least as a first step,
chemical shift values are used to generate torsion-angle restraints
using the program Talos-N (https://spin.niddk.nih.gov/bax/software/TALOS-N/).
The restraints are then used along with distance restraints in initial
structure determination. A simple script for an initial calculation
can be found in the file xplor-nih-tutorial-2018/gb1_simple/fold_nordc.py
in this link: http://nmr.cit.nih.gov/xplor-nih/xplor-nih-tutorial.tgz
Xplor-NIH also has a few explicit energy terms which can be used to
refine directly against chemical shifts, including SpartaPot (based on
Sparta) and CSPot (based on the CamShift algorithm), but I would first
start with the standard approach for structure-determination in the
above-mentioned fold script.
best regards--
Charles
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--
================================================
Woonghee Lee, I.E.I.P., M.S., Ph.D.
Assistant Scientist
and
Principal Investigator
National Magnetic Resonance Facility at Madison (NMRFAM)
and Biochemistry Department
University of Wisconsin-Madison
DeLuca Biochemistry Laboratories
433 Babcock Drive Rm B160E
Madison, WI USA 53706-1544
[email protected]<mailto:[email protected]>,
[email protected]<mailto:[email protected]>
Office: +1-608-263-1722
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