update docs to describe --unmasked-radius

docs/quickstart.md

@@ -111,6 +111,7 @@ matchmaps --mtzoff apo_data.mtz Fobs SIGFobs \
 
  - `--on-as-stationary`: The `matchmaps` algorithm always involves an alignment in real-space of the "on" and "off" maps. By default, the "off" map is stationary, and the "on" map is moved. This is typically desired, such that everything lines up with your "off" structural model. However, say that your structures are "apo" and "bound", and you would like to line up your maps with a "bound" structure (which you never have to supply to `matchmaps`!). In this case, you could use the `--on-as-stationary` flag.
  - `--dmin`: The input `mtz` files are truncated to equal resolution by default. If you would like, the `mtz`s may be truncated even more stringently.
+ - `--unmasked-radius`: How far away from the protein model do you expect to see difference signal? Use this flag to change the behavior of the `_unmasked` difference map output to show more or less signal far from the protein. Defaults to 5 A. See [below](#important-map-outputs) for more details.
  - `--spacing`: This flag defines the approximate size of the voxels in your real-space maps. The default (0.5 A) is fine for most purposes. For making figures in PyMOL, you might want finer spacing (0.25 A or so); this comes at a cost of much larger file size. If your computer/coot is being really slow, you could consider increasing the spacing.
  - `--verbose`: Use this option to print out to the terminal all of the log output from CCP4 and phenix. This is disabled by default because it's very annoying, but it can be useful for debugging purposes.
  - `--rbr-selections`: When doing rigid-body refinement, refine as multiple explicitly defined rigid bodies rather than a single rigid body containing everything. This flag is admittedly a little finnicky; please [file an issue](https://github.com/dennisbrookner/matchmaps/issues) if you have any trouble.
@@ -125,8 +126,8 @@ Below is a quick tour of the output files that `matchmaps` will produce and what
 
 Let's assume that your input files are called `off.mtz` and `on.mtz`. The following files created by `matchmaps` may be of interest:
 
- - `on_minus_off.map`: This is your difference map! It should contain positive and negative signal in the vicinity of your protein model.
- - `on_minus_off_unmasked.map`: The same as the previous difference map, but before a solvent mask was applied. This file can be useful if you're expecting signal far (>5 A) away from your protein model. Please note that the behavior of this particular file may change in the near future.
+ - `on_minus_off.map`: This is your difference map! It should contain positive and negative signal in the vicinity (>= 2 Angstroms) of your protein model.
+ - `on_minus_off_unmasked.map`: The same as the previous difference map, but before the 2 A solvent mask was applied. This file can be useful if you're expecting signal (perhaps a bound ligand) far away from your protein model. By default, this map contains signal up to 5 A away from the protein model; this radius can be changed with the `--unmasked-radius` flag for `matchmaps` and `matchmaps.mr` utilites. 
  - `on.map` / `off.map`: The real-space maps which are subtracted to produce the above difference maps. It is a good idea to open these files and inspect them. They should be generally aligned in space. Any interesting signal you expect to see in a difference map may also be apparent by inspecting these maps. Remember that both of these maps were computed using the "off" model, so structural features of the "off" data are likely to be more prominent.
  - `on_before.map` / `off_before.map`: The real-space maps, prior to alignment. These maps may be useful a) if you're curious how much alignment was necessary, or b) to troubleshoot where in the pipeline something went wrong.