ProPrep 1.23.0

Added

• Molecular Docking (main menu, Simulate stage): dock a ligand into the
  loaded structure with AutoDock Vina, scored by Vina, Vinardo or AutoDock4
  (maps from autogrid4), with ligand and receptor prepared by Meeko and
  Gasteiger charges only; no force-field parameters are needed. The ligand
  comes from a residue of the structure (its Chemical Component Dictionary
  entry placed on the crystal coordinates, an inconsistent entry reported
  atom by atom), a SMILES string, or a file loaded with the Structure Loader
  (its new option 4 loads SDF, mol2 or SMILES files and libraries). The
  dashboard walks the decisions in order: receptor and chains (alternate
  locations chosen residue by residue), the ligand, which HETATM residues
  stay in the receptor (distances to the ligand, waters within a
  hydrogen-bond distance listed with their contacts), protonation from
  pdb2pqr/PROPKA and chain ends from REMARK 465, SEQRES or OXT (asked when
  the file says nothing), metal charges and cofactor chemistry, flexible
  side chains, rotatable bonds, the search box and the settings. Bond
  orders, charges and rotatable bonds are edited by typed commands or by
  picking atoms and bonds in the viewer, where each table's rows are drawn
  and numbered. A run compares every pose with the crystal ligand when there
  is one. A docking campaign (c) docks every ligand of a library into the
  same receptor, box and settings, with the per-ligand questions answered
  once as recorded policies, resumes after an interruption, and ranks the
  ligands. Validated by redocking (biotin in streptavidin 0.35-0.77 A,
  indinavir in HIV-1 protease 0.28-0.33 A) and a protease campaign in which
  all seven inhibitors rank above all five decoys. Its dependencies (RDKit,
  gemmi, Meeko 0.8.0, AutoDock Vina 1.2.7, autogrid) are now ProPrep
  dependencies; Meeko comes from the mjgplab channel built without prody,
  which conda-forge cannot install on Apple Silicon with Python 3.12 or
  newer (packaging/meeko-noprody).
• Startup notice of a newer release. When a newer ProPrep release is on
  GitHub, the lines under the banner give its version, the one update
  command that fits how this copy was installed (the installer with -u
  for installer copies, the install script for the ProPrep conda
  environment, the in-place updater for an AmberTools environment) and the
  release page. Nothing is downloaded or changed, and the request carries
  nothing about the user. GitHub is asked at most once a day (the answer is
  kept in ~/.proprep/update_check.json, since a workshop room shares one
  address and GitHub's limit is per address); startup waits at most 1.5 s
  for the answer and says nothing when offline. Installer copies are told
  only once their platform's installer is attached to the release. The
  first check says how to turn it off: Preferences, option 4. Only copies
  built by the mjgplab conda recipe check at all: the recipe writes
  CHANNEL = "mjgplab" into proprep/_distribution.py at build time, and
  the source tree, and so the AmberTools build, keeps CHANNEL = None, so
  ProPrep inside AmberTools never points its users at ProPrep's own
  releases. The installers mark their install directory
  (.proprep_installer) so the notice can give the installer command.
  Preferences gains option 4 (Reset moves to 5, Back to 6).
• Structure viewer: an "Axes" button under View Controls draws the X, Y
  and Z axes of the coordinate frame as labelled arrows from the origin,
  each reaching just past the far edge of the structure along its axis,
  and takes them away again. NGL frames every structure the same way
  whatever its coordinates, so a structure the Structure Orientation module
  had rotated onto its principal axes looked exactly like the original.
  The colours are chosen by computed contrast for the dark, black and white
  backgrounds and follow the background when it is cycled; each letter has
  a border in the opposite tone so it reads over the molecule. The setting
  is saved with a scene and restored from one. The Structure Orientation
  module turns the axes on before and after it aligns a structure, in place
  of four unlabelled spheres 15 A out along each axis, which sat inside any
  protein of ordinary size and were never seen.

Changed

• Alternate locations: the Structure Fixer's per-residue picker (occupancy,
  atoms covered, a partial alternate completed from another, viewer
  colours) is shared with Molecular Docking, and the viewer selections now
  carry insertion codes.
• Topology Generator: the PDB is no longer reordered before tLEaP, and
  the "Configure molecule grouping for AMBER?" question no longer appears
  when tLEaP runs. sander and pmemd need every bonded unit (a chain plus
  the cofactors bonded to it) to be one contiguous block of atoms, and
  tLEaP writes ATOMS_PER_MOLECULE as if that were already so; the ParmEd
  validation after every build repairs it with rediscover_molecules and
  saves the prmtop and rst7 as a matching pair, which made the pre-build
  reordering a second mechanism for the same problem. Its analyzer also
  misread packed membrane systems (every water chain typed as protein,
  lipid residue numbers colliding with protein ones). The reordering code
  is kept, uncalled. ParmEd now also writes <name>_parmed.pdb next to
  the topology, a PDB in the topology's atom order, since after a reorder
  the PDB tLEaP read no longer matches the prmtop. Sessions recorded with
  the old questions will find them missing on replay.

Fixed

• Installing ProPrep over AmberTools 26 (the install script, the installers,
  the AmberTools updater) left inside the package the files that only
  AmberTools' bundled ProPrep 1.0.0 had: 35 of them, among them a retired
  built-in MD workflow (protein_equilibration) the MD Manager still
  offered, old MD templates, a backup module and old heme and Fe4S4
  parameter files. Every install path now removes the files ProPrep's conda
  package does not own (python -m proprep.utils.bundled_copy). An existing
  installation is cleaned by updating it: run the install script again and
  choose 1 (Update), run the new installer with -u, or run
  update_proprep_in_ambertools.sh for an AmberTools environment.
• Structure Fixer: an alternate location that models only part of a
  residue was offered as an ordinary choice, and choosing it dropped every
  atom it did not model; on the 0.80 A lysozyme 8ZST that removed the
  C-terminal leucine's backbone and left tLEaP closing the chain with a
  3.79 A peptide bond. The picker now shows how many atoms each alternate
  models, flags a partial one, and completes it from the alternate with the
  highest occupancy that has the missing atoms. Alternate labels left on
  retained atoms (lone labels, waters) are cleared too.
• Topology Generator: it builds from the Structure Orientator's output when
  there is one. The oriented structure was ranked where it could never be
  chosen, so orienting a structure did not change what tLEaP built.
• Topology Generator: tLEaP's errors and warnings are reported from the
  current run only. tLEaP appends to leap.log, so a clean build printed its
  summary of zero errors above errors left by earlier runs in the same
  folder.
• Install commands list conda-forge before salilab and bioconda. With
  salilab and bioconda first, 1.22.0 did not install on Linux under strict
  channel priority (Miniforge's default): AmberTools 26 needs RDKit, which
  bioconda has only as 2015-2016 Python 2.7 builds for Linux, and
  conda-forge's MPI fftw, where salilab has fftw 3.3.4. Changed in the
  install script, the README, the AmberTools updater, the installer recipe
  and the release build.
• Structure viewer in the terminal: an open browser tab now follows the
  viewer when a module shows other structures or re-reads edited files. The
  restarted server began its version count at 1 again, which an untouched
  page already held, and the page never reloaded structures; and a restart
  asked for port 8765 again, moving to another port when 8765 was taken and
  leaving the tab on a dead one. Each server start now has an id the page
  reloads on (keeping the camera when the files are the same), and a
  restart reclaims its port.
• Structure viewer: a view a module shows on request (the Redox Site
  Detector's view, a docking pose) opened a new browser tab every time,
  so a session collected tabs; a tab now opens only when none is open or
  loading, and the open one updates in place. A viewer server could also
  keep running unrecorded after a failed launch, leaving two in one session;
  a started server is now recorded at once, and a server whose thread died
  has its port closed. And with the main menu's Structure Viewer opened
  first, no module's views or highlights reached it (the Structure Viewer
  and the modules each had their own viewer, and updates went to the one
  that had started nothing); the modules' viewer now takes the open viewer
  over, on the same port, and the tab updates in place.
• Transformer Creator: drop takes back the last operation. Its undo
  could never run: typing undo at any prompt rewinds the session first.
• Structure Aligner: a second alignment in the same session started with
  the previous run's list of ions and waters to add and its transformation
  matrices. Both are keyed by a structure's position in the run's list, so
  they named whatever structure now held that position. The second
  redox-site alignment of calmodulin 1CLL against 2LL6 therefore re-added
  the first run's two Ca2+ and two waters, and put them into the reference
  copy (1CLL_noH_aligned_2.pdb gained residues A:293-296 on top of the
  originals) while the target got only the four it asked for. Both
  alignment entry points and cleanup() now forget the previous run.

Installers

Self-contained installers (conda not required). Download, then bash ProPrep-1.23.0-<OS>.sh. Register for a free academic MODELLER key and put it in ~/.proprep/modeller_key, or run KEY_MODELLER=<key> bash ProPrep-1.23.0-<OS>.sh at install time.

SHA-256:

aa8d1a1a2a2fb26aa68e19fd363ae419e90f3380669c062c7c93d970716096dc  ProPrep-1.23.0-Linux-x86_64.sh
40bc15d54da0bf358167cacb114d43b908916d5ba08ada182f9eacd941e06538  ProPrep-1.23.0-MacOSX-arm64.sh
59b199c76a4778f9cc6a06f5d0f95c671b4a009d21e63490840b5d1b573e9244  ProPrep-1.23.0-MacOSX-x86_64.sh