Sometimes pointing-and-clicking just doesn’t cut it. With PyMOL’s built-in Python interpreter, repetitive actions are made simple.
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Turning MD Trajectories into Movies using PyMOL
Putting movies into your presentations is the perfect way to cover up a terrible underlying presentation help the audience visualise the systems you are discussing. Static protein movies can enhance an introduction or help users understand important interactions between proteins and ligands. PyMOL plugins, such as emovie.py, help you move beyond the ‘rock’ and ‘roll’ scenes in PyMOL’s movie tab. But there ends the scope for your static structures.
If you want to take your PyMOL movie making skills to the next level, you should start adding some dynamics data. This allows your audience to visualise how your protein dynamics evolve over time and a much easier way to explain your results (because, who likes 10,000 graphs in a presentation!? Even if your R plots look super swish.). For example: understanding binding events, PPIs over time or even loop motion.
The following tutorial shows you how to turn a static PDB structure into a dynamic one, by adding a GROMACS trajectory. Most of the commands you will encounter while making a static structure movie, so should not be too alien.
Making small molecules look good in PyMOL
Another largely plagiarized post for my “personal notes” (thanks Justin Lorieau!) and following on from the post about pretty-fication of macromolecules. For my slowly-progressing confirmation report I needed some beautiful small molecule representation. Here is some PyMOL code:
show sticks set ray_opaque_background, off set stick_radius, 0.1 show spheres set sphere_scale, 0.15, all set sphere_scale, 0.12, elem H color gray40, elem C set sphere_quality, 30 set stick_quality, 30 set sphere_transparency, 0.0 set stick_transparency, 0.0 set ray_shadow, off set orthoscopic, 1 set antialias, 2 ray 1024,768
And the result:
Beautiful, no?
Good looking proteins for your publication(s)
Just came across a wonderful PyMOL gallery while creating some images for my (long overdue) confirmation report. A fantastic resource to draw sexy proteins – especially useful for posters, talks and papers (unless you are paying extra for coloured figures!).
It would be great if we had our own OPIG “pymol gallery”.
An example of one of my proteins (1tgm) with aspirin bound to it:
