Using XLIST to identify short distances for candidate NOE assignments

Basic usage:

1. Type 'xlist' to start program (/usr/local/bin must be in your search path). I usually run the program from the directory of my current stage of DYANA refinement.
2. Answer prompts asking for filenames of chemical shift list and distance file (defaults are set to 'finalar2.prot' and 'CalcDist.txt', so if these files are in your current working dir, just hit return at each prompt)
3. Follow instructions to retrieve distance (d residue_number) or shift (s residue_number) information for any residue in the protein. Chemical shift assignments for this residue will be displayed, or close distances between all protons of the specified residue and all other residues of the protein (often a long list).

To prepare updated CalcDist file:

1. Load most recent ensemble of DYANA structures into MOLMOL (ReadDG)
2. Select all 1H atoms (SelectAtom '@H*')
3. Calculate distances between all nearby atoms (CalcDist; set values as desired in dialog window; defaults are OK, but I usually increase the distance to 6 Angstroms; sometimes higher in order to find new long-range NOEs). Make sure 'report' button is checked before clicking 'OK'
4. Report window should pop up; once it is complete, click the 'Save' button. By default, it will save the file 'CalcDist.txt' in the directory from which MOLMOL was invoked.

Other notes:

1. xlist source code (xlist.f) is located in ~volkman/bin.
2. xlist can be recompiled easily (if you want to change the filename defaults, for instance). Copy source code to your dir, modify and recompile with g77:
   g77 -o xlist xlist.f