ProPrep 1.18.0

Removed

• Membrane Builder: the "preset composition" menu and its ten named
  membranes (mammalian, bacterial, mitochondrial, thylakoid, ER, yeast).
  They were ProPrep's own lipid strings and ratios with no literature
  source behind them, and two used lipid names that packmol-memgen's
  database does not contain (TLCL2; MGDG, DGDG, SQDG). The in-panel
  "common starting points" list is gone for the same reason. Compositions
  are built from packmol-memgen's own lipid database, entered as a raw
  string, or set to solvate-only, as before. The lipid library's category
  blurbs ("common in bacterial membranes" and the like) are replaced by a
  charge summary computed from memgen.parm, and three categories that
  matched nothing in that database (glycolipids, ceramides, ether lipids)
  are gone with the names they listed.

Added

• Redox Site Detector: the template results table now shows, for each
  site, the residue that was farthest from the search boundary when it was
  added, and warns when a residue belongs to more than one site. A
  count-based search always returns the requested number of residues, so a
  heme missing one axial His (a truncated multiheme chain) silently took the
  next-nearest His, which already belonged to the neighbouring site; every
  row still read ✓ because the only check was on bond length. The site
  summary lists each residue's search distance as well.

Fixed

• Banner and proprep --version read the checkout's pyproject.toml when
  ProPrep runs from source. An editable dev install keeps the package
  metadata of the version it was installed at, so the banner said 1.16.0 on
  the 1.17.0 tree; the lockstep check now warns when that metadata lags.
• ONIOM Preparer: the suggested QM (model-system) charge pooled MM partial
  charges over every selected fragment and rounded once. Whole residues
  sum to integers, but a side chain trimmed at CA-CB does not (ASP -0.86,
  GLU -0.88), so four trimmed carboxylates pooled to -3.43 and were
  suggested as -3 instead of -4. Each fragment is now rounded to its own
  formal charge and the integers summed. The on-screen note now says what
  is counted: the selected residues and side chains, with the formally
  neutral capping groups (promoted C=O or N-H plus the link H) excluded.
• Redox Site Preparer: side-chain atoms moved into a heme residue (the Cys
  and His migrations of the c-type heme transformers) were written one
  column short. The framework cleared the insertion code by splicing an
  empty string into column 27, deleting the column and shifting x/y/z left
  by one; fixed-column readers survived only by absorbing a trailing space,
  and a coordinate such as -106.695 would have lost its sign. A His claimed
  by two sites went through the splice twice and its coordinates became
  unparseable, stranding its ring atoms as a separate HEC residue and
  failing workspace validation. The chain and insertion-code fields now
  always keep their one-column width.

Installers (no conda required)

Download the file for your platform, then bash ProPrep-1.18.0-<OS>.sh. MODELLER needs your own free academic key; see INSTALL.md.

SHA-256
33ea949456bcb10514fe3a636224969d6d078b73ba841b945bd68944eae0a544  ProPrep-1.18.0-Linux-x86_64.sh
0021257fd394ec70d936db5b1f98de4d3a832e981c1d6e0355fa4b95219f7964  ProPrep-1.18.0-MacOSX-arm64.sh
1af81d97eb059dbf0c0583c7913217545e79485d78cb61ee8dd6e7a7ba39c4a2  ProPrep-1.18.0-MacOSX-x86_64.sh