refer_2_me

TIL Damian is not a mime.

Computational chemist in industry here.

Of the 3, I definitely like PyMOL the best. The ability to write pymol scripts in native python is a huge advantage. I've tried writing scripts in both VMD (mostly unsuccessfully after tons of work) and in Chimera (difficult but it ultimately worked).

In terms of looking at large simulations or a large number of simulations, VMD handles the best, but in almost all other respects, it kind of sucks.

Maestro from Schrodinger is ok in general, but I've had some problems with it when I've had around 10 MD simulations loaded.

As an aside, I'm a computational biologist/chemist and I learned programming through the exact same route. I had 1 year of Java in undergrad and then I picked up Python/bash/etc in grad school.

Same here, I was the only biologist in a pack of CS majors.