Striving for greatness

Thoughts on emerging tech, open source, and life

[Gentoo] Packaging science apps

I was just looking at my recent commits via CIA and noticed that I’ve packaged 15 new apps since Thursday, in addition to doing fonts for Xorg 7RC4. If you haven’t read this before, you may have missed my constant rants about how much science apps suck to package. The number greatly belittles the work that went into it.

A quick summary of the new apps:

Caver: Finds paths from protein cores to the surface to figure out how stuff gets in there
Maxit, Validation, PDB-Extract: Fixing PDBs (Protein Data Bank), converting to and from mmCIF
Sparky: NMR (Nuclear Magnetic Resonance) assignment and integration
Eden: Crystallographic electron-density refinement tool
Ortep3: Plots anisotropic B-factors (In human words, atoms vibrate differently in different directions)
Platon: A multipurpose crystallographic tool — calculates data from SHELX output, also graphics, etc
MAID: Automatically fits alpha-carbon chains to electron-density maps, with up to 85% accuracy

For those of you counting, the rest of the 15 come from dependencies of the above apps.


Written by Donnie Berkholz

December 19, 2005 at 11:30 pm

Posted in Uncategorized

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