More on pyMOL

The people from pyMOL responded to my last post, where I made a comment that DeLano is “heavily trying to commercialize” pyMOL. I felt I should write a little more on that.

Firstly, I wasn’t really passing judgement. There’s nothing wrong with commercial software, I’ve written enough of that myself. Nor is there anything wrong with soliciting contributions to open source software projects, especially when they’re as good as pyMOL. However, looking at the pyMOL website and download page, it seems that DeLano Sc. is trying to create the impression that a subscription is necessary. There’s a list of commercially available builds and bunch of ways to get inferior or education-only versions. The source download is right there at the bottom, but I somehow missed that when I first went to the site and I know of at least two other people who where also confused. All the options are obvious now, but it is a bit misleading for a first-time user.

I guess it’s the old problem of how to get people to contribute to open source project, and the approach is much like MySQL’s. I’m not sure how useful it is, though. A student using pyMOL once or twice for assignments is not going to pay for it anyway. Any researcher or institution, OTOH, will learn quickly that there’s a OSS version available. They’re used to open source, so there shouldn’t be much corporate red tape that can be avoided with buying commercially, nor will they afraid of compiling it themselves or require much support. The actual value of a subscription is therefore quite low, and many will just choose to pay to support the project.

There is, then, not much use in misleading people into thinking the OSS version is inferior, or hiding it below a long list of commercial options. There’s nothing wrong with asking people for a little goodwill, and many will happily do so especially when it’s not their own budget. I just wished DeLano where a bit more open about it.

Update: the response by pyMOL below is worth reading.

Measuring Angles in PyMOL

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:

1. Select Wizard -> Measurement from the main menu
2. (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”.
3. 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.