Appion

something we've been talking about for a long time:

currently, we are only able to do a single alignment iteration for any stack. One way we can do an iterative alignment is by creating a link button for every aligned stack that would upload it to the database as an original stack. This way, once an aligned stack has been created, the user has the option of uploading it as an "original" stack, then realigning it to get a finer result.

this has some caveats. For example, each program has it's own way of monitoring previous alignment parameters before applying the new ones. SPIDER needs a formatted doc file, IMAGIC stores the information in the headers (which gets lost, by the way, when we reprocess the stack with, for example, EMAN), etc. Probably what we would need to do is create a separate, Appion-specific doc file for each alignment iteration, then translate it to the program-specific parameter file.

further ideas are welcome