Appion

Attaching a solution for modifying protomo param file with user provided values.
The prototype param file is read into a string. It contains keys which are replaced with the user provided values and then written out to a new file.

There is a lot left to do, but protomo2aligner will run right now. It still needs a bunch of stuff added to it. I put comments in the code about the direction I think the script should take. One thing I'd really like to do is have the tomography scripts make animated gifs instead of flash movies. That will reduce dependencies and make something that is exportable. I uploaded some free code I found for generating animated gifs from numpy arrays using PIL. I would love to work on protomo2aligner more, but I don't have the time to do it right. Can I hand it off to you Amber? I will be happy to continue to work with you closely to get it working.

This feature is replaced by #2834