Measuring Angles in PyMOL
Posted: January 8th, 2009 | Author: Matt | Filed under: Bioinformatics | Tags: Bioinformatics, pymol, visualization | 2 Comments »PyMOL is probably one the coolest molecular visualization tools there are, but the interface is sometimes a little awkward. This is how to measure a bond angle in PyMOL:
- Select Wizard -> Measurement from the main menu
- (This is the non-obviousness) The headline “Distance” in the toolbox in the lower right-hand corner is actually a dropdown. Click on it and select “angle” or “dihedral”.
- Click on any three (four for dihedrals) atoms that define the bond you want to measure.
Additional tip: the people behind PyMOL are heavily trying to commercialize it, but free versions are available here. They call those versions “outdated”, but there’s nothing wrong with them.
Quote: “the people behind PyMOL are heavily trying to commercialize it…”
Are you sure that’s correct? If those people really wanted to commercialize PyMOL, then why would they still be giving current PyMOL source code away FOR FREE?
And why would they still be directing users to their hosted downloads of “outdated” PyMOL versions FOR FREE?
Any why would they still be giving out current PyMOL builds away to students and teachers FOR FREE?
If the people behind PyMOL actually wanted to commercialize it, then they could simply take their next version closed-source and stop giving away all those FREE builds which, as you correctly point out, have absolutely “nothing wrong with them”.
So give ‘em a little credit, will ya?
It would be much more fair to say: the people behind PyMOL are heavily trying NOT to commercialize it, while still generating enough revenue to fund the project. How? By convincing users who actually do have discretionary funds to make recurring contributions in support of the effort.
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