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Update PDB id handling so that it uses the new PDB id structure

Status: Open.

#228 In diff-use/sampleworks;

· marcuscollins opened on Apr 29, 2026

Migrate to selection-first approach in classify_altloc_selections.py

enhancementNew feature or requestNew feature or request

Status: Open.

#226 In diff-use/sampleworks;

· k-chrispens opened on Apr 22, 2026

Our tests appear to require access to some remote server, and we sometimes get timeouts

bugSomething isn't workingSomething isn't working

engineeringTask that is best suited to software engineers, not research scientistsTask that is best suited to software engineers, not research scientists

Status: Open.

#216 In diff-use/sampleworks;

· marcuscollins opened on Apr 10, 2026

Selection strings used in evaluation scripts should specify which set of labels they are selecting on.

CIF issuesAll issues related to the writing, reading, or parsing of CIF files or objects.All issues related to the writing, reading, or parsing of CIF files or objects.

engineeringTask that is best suited to software engineers, not research scientistsTask that is best suited to software engineers, not research scientists

Status: Open.

Feature

#215 In diff-use/sampleworks;

· marcuscollins opened on Apr 10, 2026

CIF file outputs should maintain the original file(s)' label_seq_id, auth_seq_id numbers and chain letterings

CIF issuesAll issues related to the writing, reading, or parsing of CIF files or objects.All issues related to the writing, reading, or parsing of CIF files or objects.

engineeringTask that is best suited to software engineers, not research scientistsTask that is best suited to software engineers, not research scientists

enhancementNew feature or requestNew feature or request

Status: Open.

#214 In diff-use/sampleworks;

· marcuscollins opened on Apr 10, 2026

Evaluation scripts should get the locations of maps or input pdb files used from the results metadata, not from a config file or command line arguments

CIF issuesAll issues related to the writing, reading, or parsing of CIF files or objects.All issues related to the writing, reading, or parsing of CIF files or objects.

engineeringTask that is best suited to software engineers, not research scientistsTask that is best suited to software engineers, not research scientists

Status: Open.

#213 In diff-use/sampleworks;

· marcuscollins opened on Apr 10, 2026

Output metadata should be updated to include start and end time from JobResult

CIF issuesAll issues related to the writing, reading, or parsing of CIF files or objects.All issues related to the writing, reading, or parsing of CIF files or objects.

engineeringTask that is best suited to software engineers, not research scientistsTask that is best suited to software engineers, not research scientists

good first issueGood for newcomersGood for newcomers

Status: Open.

#212 In diff-use/sampleworks;

· marcuscollins opened on Apr 10, 2026

Evaluation scripts should read metadata either from the job_metadata.json file or directly from the output CIF

CIF issuesAll issues related to the writing, reading, or parsing of CIF files or objects.All issues related to the writing, reading, or parsing of CIF files or objects.

engineeringTask that is best suited to software engineers, not research scientistsTask that is best suited to software engineers, not research scientists

Status: Open.

#211 In diff-use/sampleworks;

· marcuscollins opened on Apr 10, 2026

Address ty warnings so we can undo the changes to the tools.ty section in pyproject.toml in #189

engineeringTask that is best suited to software engineers, not research scientistsTask that is best suited to software engineers, not research scientists

enhancementNew feature or requestNew feature or request

Status: Open.

#197 In diff-use/sampleworks;

· k-chrispens opened on Mar 30, 2026

Fix chain lettering mismatches in output CIF files for protenix

Status: Open.

#193 In diff-use/sampleworks;

· marcuscollins opened on Mar 27, 2026

Refactor annotate_structure_for_wrapper_type as a util method rather than a method in tests/conftest.py

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

Status: Open.

#192 In diff-use/sampleworks;

· k-chrispens opened on Mar 27, 2026

More stringent atom ordering tests in tests/models

enhancementNew feature or requestNew feature or request

Status: Open.

#191 In diff-use/sampleworks;

· k-chrispens opened on Mar 27, 2026