Im conducting a number of superpositions (match maker in Chimera) on large protein structures. I was wondering if these superpositions can be parallel processed? So I have a number of superpositions running at once?
You could run multiple Chimeras at once. How you do that depends on what kind of machine you're on. You should probably ask this question on the chimera-users mailing list (http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html) for the best answer.
For protein superposition I would more likely use some software like Profit that is not only more likely to be faster but also easier to parallelize.
if you're doing lots of structure superimposition, you may want to look into tools designed specially for that (ie: MAMMOTH).
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version 2.3.6
First, why Chimera? You should use the structure superposition program most appropriate for your task. Things that affect the program choice is expected structural difference between the proteins, whether they have different sequence, and whether you want to create multiple structure superposition. E.g. for remote structures choose TM-Align, for multiple structure superposition of proteins with detectable sequence similarity choose Theseus. Last, maybe this ultra-fast method fits your needs: http://theobald.brandeis.edu/qcp/