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Published June 14, 2024 | Version 0.7.0
Software Open

SBC-Utrecht/pytom-match-pick: 0.7.0

  • 1. Utrecht University
  • 2. Max Planck Institute for Molecular Physiology

Description

This is a big one! And probably containts the last major api changes before the 1.0.0 release.

Wiki/tutorial will soon be updated to correspond with latest changes.

Main updates

  • Thanks to @sroet the package now supports arbitrary angular sampling generation via healpix. This now makes it possible to provide a particle diameter as input and let pytom-match-pick figure out the correct angular sampling!
  • A bug was fixed in the particle symmetry option as it was not applied to the correct euler angle.
  • CTF parameters can now only be applied in pytom_match_template.py and no longer for template creation. This makes input more consistent and logical.
  • Particle lists can be written out to be Relion5 compatible: centered coordinates in angstrom and proper star file column names.
  • A tomogram mask can be provided during template matching and will skip subvolumes where the mask is empty.

PRs

  • Readme illustration by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/156
  • Phase plate ctf and argparse grouping by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/157
  • default value phase shift entry point by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/159
  • Update cupy requirements by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/167
  • wait longer to prevent leaked processes by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/168
  • small speedboost by precalculating conjugation by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/165
  • expose tophat kernel connectivity and make n-false-postives a float by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/166
  • make template non-symmetrical for template matching test to prevent race condition by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/169
  • refactor volume splitting by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/170
  • auto generate sampling angles by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/163
  • Ctf rework by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/174
  • Relion5 compatibility by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/178
  • Center of mass fix by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/179
  • calculate angular search from particle diameter by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/181
  • fix symmetry bug by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/184
  • phase randomization score map correction by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/182
  • pre-commit with ruff by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/183
  • Add tomogram mask option for template matching by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/185

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.6.0...0.7.0

Files

SBC-Utrecht/pytom-match-pick-0.7.0.zip

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