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