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Recommend repairing the structure with PDB2PQR before PROPKA and Prodes #33

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Merged
teese merged 8 commits into from
Sep 12, 2026
Merged

Recommend repairing the structure with PDB2PQR before PROPKA and Prodes #33

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9c40b28
Recommend repairing the structure with PDB2PQR before running PROPKA …
teese Sep 11, 2026
f4d24b0
Warn about the multi-chain pKa warnings and about selecting features …
teese Sep 11, 2026
508e234
Install PDB2PQR in its own environment instead of alongside Prodes
teese Sep 12, 2026
7efea15
Ignore the per-repo direnv file and single-investigation Python scripts
teese Sep 12, 2026
fb54c05
Record what repairing a predicted structure does, and how the termina…
teese Sep 12, 2026
07c0a3a
Shorten the note on how the terminal oxygen is scored
teese Sep 12, 2026
e572afe
Pass --keep-chain when repairing a structure, and record which output…
teese Sep 12, 2026
4fe8fed
Reconcile the structure preparation documentation with version 9.0
teese Sep 12, 2026
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4 changes: 3 additions & 1 deletion .gitignore
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Expand Up @@ -21,8 +21,10 @@ docs/similar_tools/*
# wrong. Anything worth keeping belongs in a docstring, the README, or an issue.
# Name them so the intent is visible in a file listing, for example
# plan_thing_notrack.md or plan_thing_REVIEW1_notrack.md. Use git add -f to
# commit one deliberately.
# commit one deliberately. The same applies to a script written to answer one
# question, which is superseded as soon as its answer is recorded.
*_notrack.md
*_notrack.py

# APBS comparison outputs and the capture file APBS writes into its working directory
apbs_results
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