v0.6.5

Important changes

• matchmaps now supports both phenix 1.20 (and earlier, though I'm not sure how far back it goes) and the new phenix 1.21 syntax. matchmaps will attempt to automatically detect the user's phenix version based on the output from phenix.version, but the user can override this if it is wrong for some reason (e.g. multiple phenixes are present or something).
• Previously, when CCP4 or phenix subprocesses failed, and the program was not being run in verbose mode, these failures were totally silent to the user. The failure then manifested as an unhelpful FileNotFoundError. Now, the user is specifically informed of which subprocess has failed, and is instructed to use verbose mode for more information.

Abbreviated Changelog

• Add support for phenix 1.21 by @dennisbrookner in #53
• Refactor argument parsers to avoid duplication by @dennisbrookner in #55
• clarify that phenix 1.21 is supported by @dennisbrookner in #56
• Helpful error detection from sub-processes by @dennisbrookner in #58

Full Changelog: v0.6.4...v0.6.5

v0.6.4

What's Changed

• Drop support for python 3.8 by @dennisbrookner in #52

Documentation changes

• Add troubleshooting / advanced usage page to website by @dennisbrookner in #49
• link to paper rather than preprint by @dennisbrookner in #50

Full Changelog: v0.6.3...v0.6.4

v0.6.3

What's Changed

• ci(dependabot): bump styfle/cancel-workflow-action from 0.12.0 to 0.12.1 by @dependabot in #40
• Expanding the "about the algorithm" page by @dennisbrookner in #41
• ci(dependabot): bump codecov/codecov-action from 3 to 4 by @dependabot in #42
• Suppress error where scaleit fails on non-isomorphous inputs by @dennisbrookner in #44
• ci(dependabot): bump softprops/action-gh-release from 1 to 2 by @dependabot in #45
• Make explicit that phenix 1.21 is not currently supported by @dennisbrookner in #47
• bump rs-booster dependency to version 0.1.2 by @dennisbrookner in #48

Full Changelog: v0.6.2...v0.6.3

v0.6.2

This version adds support for error-weighting to matchmaps and matchmaps.mr. Various bug fixes are also included and are described below.

What's Changed

• Fix bug: unmasked_radius was parsed but ignored by @dennisbrookner in #34
• fast-forward weights branch with bug fix from main by @dennisbrookner in #35
• Weights by @dennisbrookner in #36
• ci(dependabot): bump actions/setup-python from 4 to 5 by @dependabot in #33
• Create new visualization.md page by @dennisbrookner in #37
• Fix crash when --input-dir and --output-dir match by @dennisbrookner in #39

Full Changelog: v0.6.1...v0.6.2

v0.6.1

This PR doesn't include any material change to the outputs of matchmaps. The inclusion of FoFc coefficients in phenix outputs is purely for comparative analysis and does not affect the matchmaps difference map. Changes in map normalization lead to changes in contour levels, but not in the appearance of maps themselves when viewed at appropriate contour.

What's Changed

• Phenix outputs include FoFc map coefficients by @dennisbrookner in #30
• Implement proper map normalization by @dennisbrookner in #31

Full Changelog: v0.6.0...v0.6.1

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

Support `.cif` structure inputs and fancier docs

The pre-print is out! Read it here. This is what's leading to the semi-arbitrary bumping all the way up to 0.5. Online documentation is now much more extensive.

What's Changed

• Update quickstart guide by @dennisbrookner in #21
• Support .cif inputs as alternatives to .pdb by @dennisbrookner in #23
• Update docs to link to pre-print and describe algorithm by @dennisbrookner in #24

Full Changelog: v0.4.1...v0.5.0

v0.4.1

What's Changed

• patch bug in version utility by @dennisbrookner in #20

Full Changelog: v0.4.0...v0.4.1

v0.4.0

This release brings matchmaps much closer to a final, stable codebase. #18 is a significant overhaul of the file i/o. It may have the side benefit of Windows compatibility, but I can't guaranteed this. #17 and #19 are both needed, common-sense updates to the algorithm. Additionally, #19 adds a matchmaps.version utility to print the package version to the command line. PR descriptions below.

What's Changed

• add rs favicon to site by @dennisbrookner in #16
• Implement resolution truncation between scaling and refinement by @dennisbrookner in #17
• Handle all filenames with pathlib by @dennisbrookner in #18
• Normalize by @dennisbrookner in #19

Full Changelog: v0.3.1.2...v0.4.0

v0.3.1.2

Testing release to PyPI under new repo home