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]> 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 > > ######################################################################## > > To unsubscribe from the XPLOR-NIH list, click the following link: > Bad URL Removed - see why - > https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1 > -- ================================================ *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], [email protected] Office: +1-608-263-1722 https://sites.google.com/view/wlee-group www.nmrfam.wisc.edu ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
