-- "Stirred, not shaken."

STIR is a wrapper for PyMOL that provides a collection of tools for the visualization of gromacs molecular dynamics trajectories.

Its main focus are Martini coarse-grained systems.

Grab the latest PyMOL from here. You will also have to install garnish.

Once you've done that, you can just use pip:

pip install git+git://github.com/brisvag/stir.git#egg=stir

pip will automatically add the stir command to your PATH.

Use stir to open PyMOL and automatically run all the default tools. Check out the help with:

stir -h

For example, to load a typical system:

stir system.gro topol.top md.xtc

stir initializes PyMOL with its own pymolrc and automatically runs garnish and nice. It also loads the other tools, ready to be used from within PyMOL.

Draws bonds and elastic network for coarse-grained systems.

garnish [selection [, tpr_file|top_file]]

Source: https://github.com/mjtadema/garnish

Provides a series of functions for easy selection and visualization.

Wraps other subtools to select, color and show molecules nicely.

nice [style [, selection]]

To automatically create (or delete) commonly used selections, such as lip for lipids and BB for backbone beads:

nicesele [, delete]

Color all atoms in the selection with the same random color based on a common identifier (chain id, residue name...). To see a list of all the options, check out PyMOL's iterate command.

nicecolor resi|chain|name|... [, selection]

Shows periodic images. To show a 3x3 grid in the x,y plane:

supercell 3,3,1

To show first 2 neighbouring cells in the z direction:

supercell 1,1,5

Source: https://github.com/speleo3/pymol-psico/blob/master/psico/xtal.py

Makes a nice, ray-traced picture or movie of the system. A few options are available (see help cheese). Try:

cheese snap

to take a quick ray-traced picture. For a movie, try:

cheese bullettime, test_movie, width=640, height=480

Split the system into multiple objects according to a specific rule. For example, to split protein/lipids/nucleic/solvent:

split groups