PyNMR

Attempt to add NMR abilities to molecular viewer Pymol, including :

• Display distance constraints as sticks between atoms / group of atoms with color code

• Display distance constraint density as a color gradient on the molecular skeleton

• Possibility to choose :
  • Method of distance calculation (ambiguous restraints)
  • Colors and size of NOE representations
• CNS or CYANA format available
• Command line and GUI (using Tk and Pmw)

This plugin actually works quite well, although some work is remaining.

Installation :

###For development version :

• Copy the files into a single directory anywhere on your disk
• Edit .pymolrc in your home directory and add "run /path/to/files/pymolNMR.py"
• Edit variable "installDir" in pymolNMR.py (Hopefully this should not be needed in the future)

###For user friendly version :

• Download "PyNMRPG.py"
• Use the Pymol standard plugin install in the main menu

Start plugin :

###For development version :

It is not a standard pymol plugin, so you have to type in the command line (or add in .pymolrc) : pyNMR.startGUI()

###For user friendly version :

Start PyNMR from the plugin menu.

Usage :

The GUI is quite straightforward for NMR people I think. For CLI, read pymolNMR.py.

Possible future features :

• Display of angular, dihedral and h-bonds constraints
• Text list of constraints with :
  • Color code
  • Link to 3D display
  • Real-time edit / display
• Increase speed

Known difficulties :

• When displaying a large number of constraints as sticks, Pymol performances decrease rapidly :
  • Avoid to draw all constraints if not necessary
  • Remove them before any other action if you can
• The listbox behaviour is a bit eratic for now, use it just before the display buttons.