Hi,
I have a project in ccpnmr_ver_3 in which I made the assignment of signals in the NOESY spectrum. I need to get a file with restraints
on distances and dihedral angles, for further modeling of the structure.
As I understand it, usually such restrictions are in the NEF file, but I don’t understand what I need to do to get this file. I would really appreciate it if someone would explain it to me.
Hi,
I don’t think you can go direct from an assigned peak list to a restraint list in Analysis at the moment, unless @ElizaP has a macro for this.
The main issue doing this would be how to calibrate your distances from your volumes/heights. In principle you can do this either via classes or via a proportionality constant. In either case you would have to specify which volumes/heights go into which distance class or what proportionality constant you want to use. Most structure calculation programs these days will simply take a peak list as input, do the peak assignment and calibrate the distances for you, and then provide you with the distance restraint lists alongside the structural ensemble at the end.
I know ARIA has the option to retain peak assignments. So you could export your Chain, ChemicalShiftList and PeakLists to a NEF file and set up an ARIA calculation in which you retain your assignments and then it would end up giving you distance restraint lists in return. See our NEF Tools Workshop video at
starting at 40:48 for information on how to move from AnalysisStructure to Structure Calculation programs and ARIA in particular from 42:55.
So it all depends a bit what you plan to do with your restraint lists. Do you want to use them in an MD simulation or a structure refinement as you imply (in which case you would explicitly need the restraint lists)? Or do you simply want to do a normal ab initio structure calculation (in which case you only need the peak lists and the structure calculation software will generate the restraint lists for you)?
Vicky
NEF-Piplines can do it as long as you don’t have too complicated restraints… but you would need to measure your own molecular ruler and calibrate
regards
Gary