Nice software?

I feel like blogging because it seems that my job is finally running the way it's supposed to. Let's review the software used (and complain).

There's the Python Macromolecular Library. It has tons of cool functions like telling you that your atom names are non-standard amino-acid-atom names or creating a chain with all your waters. It's a nice clean elaborate package but I think for doing so much work, they a left out important functions. For example changing fragment IDs is rather difficult or adding fragments to chains. And saving parts of a protein file in a new pdb is not convenient.

Babel and Open Babel are really nice programs but they are probably what drove me nuts most. All that changing between file types is pretty cool. But the problem is if you want specific output. Starting out with a simple parser would have probably been faster than all that messing with Open Babel and re-editing the files afterward. And where I really needed it, it failed me: for adding hydrogens. The interesting thing is that Open Babel protonated His and Arg, and Babel left both without protons. Both is of course wrong in physiological conditions. Using the pH-model function, which seems pretty nice, did not change anything.

Maybe the solution would be Open Babel in Python. You can probably do more when you are closer to the source. You can even Kekulize molecules there.