2D, 3D-NOESY Assignments

PACSY-ALIGN generates 2D, 3D-NOESY assignment files regarding aligned structure coordinates for non sequential assignments. Three 3D NOESY types, 15N / 13C / Aromatic, NOESY spectra and 2D NOESY in Sparky format are provided. Six files for each 3D NOESY type and two files for 2D NOESY in different axis orders are given. Overall 20 files are provided. They are all in the /peaklists directory inside subdirectories (e.g. 1_2LN3_A/peaklists).

Small h in the file name (CHh, NhH, …) indicates that axis is the resonance from the space. For instance, 15N-NOESY-NhH.list file is like the following:

As it can be seen, first and third axes are attached atoms, while second is from the other.

This file can be read by Read Peak List (two-letter-code: rp) in NMRFAM-Sparky. We added Label peaks function in the program for validating generated assignments.

Two methods to read in can be applied.

1. Create peaks

If user applies this method, user needs to go through peak lists and delete assignments that does not agree with peaks on the spectrum. Peaks with low intensity in the Peak List (two-letter-code: LT) can be selected to remove by new selection tool (select peaks smaller than selected peak, two-letter-code: ss) after finding the optimal noise threshold.

2. Label peaks

This is the new feature developed recently. It only labels assignments to the peaks already exist in the spectrum. Therefore, assignments that do not make sense at all, automatically will be dropped during this process.

After read-in, distance constraints can be prepared for structure calculation. Automated NOE calibration (two-letter-code: gd) or manual binning method (two-letter-code: xf) can be used.

* Generate distance constraints (two-letter-code: gd)

* XPLOR/CYANA/PONDEROSA Restraints (two-letter-code: xf)

* Simulated distance and hydrogen constraints

PACSY-ALIGN provides simulated distance and hyrogen constraints based on NOESY assignments in PONDEROSA/CYANA format. PLEASE AWARE THESE ARE SYNTHETIC DATA. They are named simulated_PDB_CHAIN.upl and simulated_hbond_PDB_CHAIN.upl in each sub directory.