Address referee comments

[jchodera]

I'm partway through this.

[jchodera]

I've finished my edits to the manuscript (edits in red) and generated a response letter (response-letter/) in Word.

@danielparton and @sonyahanson: Can you take this over now?

Remaining items:

• Go through manuscript edits and response letter (@pgrinaway too)
• Sections of the manuscript that need text from @danielparton are in orange
• We need to add a MolProbity score computation feature, and a figure based on it
• We need to add another panel to our Src/Abl order parameter figure, or a separate figure, for another kinase
• We should add the option for user-specified substitution matrices
• Now is the time to sneak in some words about any other features we have added since submission (is the YAML format ready?)
• We should add a small figure showing how many structures there are for each target
• Finally, @sonyahanson could really help with the reviewer response (see section in red) if we know that we don't have structures for some active or inactive states for Src or Abl but we do see models for these in Ensembler. Alternatively, the addition of the third kinase to Fig. 8 might be sufficient to show this.

[jchodera]

Oops. One more set of edits to check in.

[jchodera]

OK, all finished!

The referee response letter is 14 (!!!) pages long.