v0.6.0

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 #22
• ci(dependabot): bump styfle/cancel-workflow-action from 0.11.0 to 0.12.0 by @dependabot in #25
• Support sfCIF files as alternatives to MTZs by @dennisbrookner in #26
• Add --unmasked-radius parameter to change the behavior of the unmasked difference map by @dennisbrookner in #27
• Add --no-bss flag to optionally turn off bulk-solvent scaling in phenix.refine by @dennisbrookner in #28
• Write out .sh file for reproducing command by @dennisbrookner in #29

New Contributors

• @dependabot made their first contribution in #22

Full Changelog: v0.5.0...v0.6.0