Changes to solvent-region behavior
This release includes two PRs, 27 and 28 , which enhance the ability of `matchmaps` to show difference density far away from the protein model.
27 adds an `--unmasked-radius` parameter which changes the behavior of the `XXX_unmasked.map` output difference map. This map now incudes voxels up to `--unmasked-radius` Angstroms away from the protein model. **The default radius for the unmasked difference map was also increased from 3 A to 5 A; this is a semi-breaking change.** If you would like your unmasked map to look the same as it did in `matchmaps < 0.6`, set `--unmasked-radius 3`. The regular, "masked" difference map continues to be masked at 2 A away from the protein model. This PR does not introduce the ability to change this.
28 introduces the `--no-bss` flag, which allows the user to turn off bulk-solvent scaling in `phenix.refine`. For reverse compatibility, the default (no flag) continues to be that bulk-solvent scaling **is** included. This flag takes no argument, so simply add the flag to turn off BSS. The rationale for this feature is that signal for an unmodeled ligand or protein conformation may be altered by bulk-solvent scaling when this unmodeled signal lies in the solvent region. Turning off BSS can be thought of as a sort of "lazy polder map."
Two other minor changes described below:
- Reflection files may now be supplies using `.cif` files as an alternative to `.mtz` files. This makes `matchmaps` fully compatible with both mmCIF and sfCIF file types.
- `matchmaps` now writes out a shell script which can be used to re-run the same command (and of course, which can also be edited to run a slightly different command). This file is called `run_matchmaps.sh` by default; this name can be changed via the new `--script` flag. The script is written out to the ***current working directory*** to ensure compatibility with the input and output paths provided.
Auto-generated summary of changes
* ci(dependabot): bump actions/checkout from 3 to 4 by dependabot in https://github.com/rs-station/matchmaps/pull/22
* ci(dependabot): bump styfle/cancel-workflow-action from 0.11.0 to 0.12.0 by dependabot in https://github.com/rs-station/matchmaps/pull/25
* Support sfCIF files as alternatives to MTZs by dennisbrookner in https://github.com/rs-station/matchmaps/pull/26
* Add `--unmasked-radius` parameter to change the behavior of the unmasked difference map by dennisbrookner in https://github.com/rs-station/matchmaps/pull/27
* Add `--no-bss` flag to optionally turn off bulk-solvent scaling in phenix.refine by dennisbrookner in https://github.com/rs-station/matchmaps/pull/28
* Write out `.sh` file for reproducing command by dennisbrookner in https://github.com/rs-station/matchmaps/pull/29
New Contributors
* dependabot made their first contribution in https://github.com/rs-station/matchmaps/pull/22
**Full Changelog**: https://github.com/rs-station/matchmaps/compare/v0.5.0...v0.6.0