ProPrep 1.21.0

Added

• MD Manager trajectory analysis: method choices that used to be fixed inside
  the code are now yours to make. Each is a prompt with its default shown, and
  each is recorded in the session log.

  • Clustering and Pairwise RMSD: the distance between frames can be best-fit
    RMSD, RMSD without fitting, or distance RMSD. K-means asks for its random
    seed (the same seed reproduces the same clusters); hierarchical clustering
    asks for average, single or complete linkage.
  • Density maps can be accumulated in the solute's frame: molecules are made
    whole around the solute (autoimage) and every frame is fitted on a mask to
    the first frame, on a copy of the trajectory. This is what density around
    a tumbling solute needs, and it is the default; the lab frame is still
    offered. The grid point limit and the number of peaks listed are asked.
  • RMSF and B-factors ask for the alignment mask and reference frame. PCA
    asks whether to fit to the average structure.
  • Contacts and Salt bridges ask for the persistence threshold; Contact
    frequency asks for its distance cutoff; Autocorrelation asks for the RMSD
    reference frame and the maximum lag.
  • Ramachandran asks for the bounds of the alpha and beta regions and for the
    flexibility threshold; omega asks for the planarity tolerance.

• A trajectory file that stores no frame times: ProPrep says so and asks for
  the time between frames. With none given, plots use the frame number.

• Results state the definitions behind them: the charged atoms used for salt
  bridges (now including AMBER's charged histidine, HIP), the water mask
  used for water shells, how DSSP codes are grouped into helix, sheet, turn
  and coil, that vector ends are geometric centres, and that contact
  distances are not imaged.

• Structure Viewer: a structure against its electron density (option 6,
  "Launch viewer with electron density"). For an X-ray entry deposited with
  its structure factors, ProPrep fetches the two maps PDBe provides, the
  2mFo-DFc map and the mFo-DFc difference map, and shows them in the viewer
  with a new Electron Density panel: each map on or off, and its contour level
  (starting at the usual 1.0 and +/-3.0 sigma, green for unexplained density
  and red for model without density). The whole map is shown to begin with.
  To look at one place, pick a ligand, ion or cofactor from the panel's list,
  or type a selection such as 79:A or [HBI]: the view moves there and the
  density is drawn in a box around it, whose size you set. The box belongs to
  the model and stays on it when you move the view; a checkbox gives the other
  convention, used by Coot, where the box stays mid-screen and the model moves
  through it. A selection that NGL cannot read matches every atom instead of
  failing, so the panel says how many atoms matched and refuses that case.

  • For contrast, the mesh near the atoms you choose is coloured differently
    from the mesh elsewhere. Choose atoms by clicking them (one at a time or
    a whole residue per click; click again to take them out), from the panel's
    list of ligands, or with a selection; none of these needs a precise
    pointer. You set how near counts (default 2 A), the two colours, and how
    bright the rest of the mesh stays. Dimming the rest is what makes the
    difference: the default yellow on the default blue mesh is only 1.9 : 1,
    below the 3 : 1 asked of graphics, because both are bright; with the rest
    at 40%, the default, it is 7.8 : 1. The panel states the contrast ratio
    for whatever colours you pick and warns below 3 : 1. The difference map
    keeps its green and red near your atoms, since those colours carry
    meaning, and is dimmed elsewhere with the rest.
  • The maps are calculated by PDBe from the deposited data and the deposited
    model, so the 2mFo-DFc map leans towards the model; ProPrep says so, and
    the difference map is the more honest of the two.
  • A PDBe map covers one unit cell at the origin, while models mostly lie in
    neighbouring cells (no cofactor atom of 1LTZ or 1J8U is inside its map).
    ProPrep re-cuts the periodic density around the model, an exact copy of
    grid values, so density appears where the atoms are. Sigma levels are
    those of the whole unit cell, the crystallographic convention, not of the
    re-cut box.
  • Density is shown only for a structure that still lies where the entry was
    deposited: as downloaded, filtered, protonated or renamed. A structure
    superposed onto another has left its map behind. ProPrep decides this from
    the map itself (a model in its own density sits near +3 sigma on average,
    the same atoms anywhere else at 0) and tells you the number, so a moved
    structure is refused even if its file still carries the entry's header.
    NMR and cryo-EM entries, and entries without deposited structure factors,
    are told why they have no density. The margin of density kept around the
    model is asked (default 5 A).

• Structure Loader: the article behind a structure. When a structure is
  loaded, from the PDB or from a local file, ProPrep shows the publication
  recorded in the file: title, authors, journal reference, and PubMed and DOI
  links, or says that the entry was never published. This needs no internet
  connection and asks nothing. Under View structure metadata, the
  publications view adds the article's abstract and says whether a free full
  text exists and where, from Europe PMC. The abstract is often what says
  which form of a cofactor is really in the structure. ProPrep does not
  download articles: most are behind a subscription, and PubMed Central and
  the publishers refuse scripted PDF downloads, so it gives links to open in
  a browser, where your own access applies.

• Structure Loader: search the Protein Data Bank by ligand (Query Protein Data
  Bank, option 4). Enter a ligand code or words from its name; ProPrep lists
  the matching ligands and how many structures contain each. From any code it
  can then list the related ligands, because one compound is in the PDB under
  several codes: those made of the same atoms with a different number of
  hydrogens (other redox and protonation states, tautomers, stereoisomers) and
  those RCSB scores as structurally similar, each labelled with how it was
  found. Starting from tetrahydrobiopterin (H4B) this finds its 6S epimer
  BHS, the dihydrobiopterins HBI and H2B, and biopterin BIO. You type
  the codes to search for and how many structures to list; they come best
  resolution first, with the ligand code each contains and the real-space
  correlation of that ligand with the electron density. Nothing is filtered
  out for you: lookalikes are shown and labelled, and a reminder is printed
  that the code is the depositors' choice and does not always match the state
  their title describes. A search that cannot reach RCSB says so, and is not
  reported as "no results".

• Structure Viewer: "View the loaded MD trajectory" plays the topology and
  trajectory loaded with Structure Loader > Load AMBER topology & coordinate
  files. Every loaded segment is read in order as one trajectory, in any
  format cpptraj reads (NetCDF, mdcrd, DCD, XTC, TRR, binpos), and no PDB
  structure needs to be loaded. The option is available once a topology and
  trajectory are in the workspace, and says where to load them until then;
  the Structure Loader now points to it. In 1.20.0 the only way to a playing
  trajectory was MD Manager > Analyze completed simulations > a simulation >
  "Select analysis type" > 4, which is still there and shares the same code.

• Structure viewer: save a trajectory movie. The Movie panel (shown with the
  Trajectory panel; m records, Esc cancels) renders the trajectory frame
  by frame to an MP4 with the current camera, representations and background:
  frame range (backwards too), stride, interpolated in-between frames, frame
  rate, size (1-3x the viewport), quality and antialiasing. It is frame-exact
  rather than a screen recording, so it plays at the chosen frame rate however
  long a frame took to render, and H.264 MP4 opens in Keynote, PowerPoint and
  QuickTime. Encoding happens in the browser (WebCodecs; a current Chrome,
  Edge, Safari 17+ or Firefox 130+) and the file downloads like a screenshot.
  The MP4 writer (mp4-muxer 5.2.2, MIT) ships with ProPrep and is served by the
  viewer's own server, so saving a movie works offline.

• Structure viewer: a Depth cue button turns NGL's distance fog off and on.
  Off gives a cleaner figure of a small solute. The setting is saved with a
  scene.

• Structure viewer: h hides and shows the control panel, for any structure,
  so the molecule fills the window (for a figure, or a wider movie). The Hide
  Panel button was already there; the key is ignored while typing in a field.

Changed

• Every menu and yes/no question: an answer that is not accepted is now
  named. Received "'4", which is not one of the available options replaces
  "Please select one of the available options", which read as though the
  option were unavailable. The usual cause is a key pressed while ProPrep was
  busy printing: the terminal holds it and puts it in front of your next
  answer, and shows it where the cursor was at the time, not at the prompt, so
  the prompt line itself looks correct. The answer is shown exactly as
  received, so a stray quote, space or arrow key is visible. Nothing else
  changes: the question is asked again as before, and session recordings still
  hold only the accepted answer.

• Structure Loader, search by entry title: the number of structures listed
  was fixed at 100 inside the code and never mentioned. ProPrep now reports
  how many structures match, then asks how many to list (default 100, up to
  the 10,000 that RCSB returns for one search). The most relevant are kept and
  shown best resolution first, and the results heading says so. A session
  recorded before this release asks this one question live on replay, then
  carries on from the recording; Enter gives the old behaviour. With no
  internet connection the search now says RCSB could not be reached, where it
  used to report that no structures were found.

• "Protein residues" in the analysis region menu, and the default residue
  range for Ramachandran and Water shells, are read from the topology
  (residues with an N, CA, C backbone). They were a guess (the first 80% of
  all residues, or residues 1-500), which in a solvated small system is mostly
  water.

• DSSP widens an atom selection such as C-alpha to the whole protein residues
  it touches, and says so; DSSP cannot find backbone hydrogen bonds otherwise.
  Secondary structure is assigned with the whole protein present and the
  selected residues are reported: assigned on a partial selection alone, a
  residue whose hydrogen-bond partner lies outside the selection was
  misassigned. The notes that DSSP needs a separate dssp executable were
  wrong (it is cpptraj's own) and are gone.

• DSSP is run by the cpptraj program, not through pytraj. On Linux, pytraj's
  DSSP call damages the program's memory, and ProPrep then stopped without
  warning at a later analysis: in the Linux installer, DSSP followed by other
  analyses ended the session in 11 of 20 tries, against 0 of 20 without DSSP.
  The cpptraj program gives identical assignments and ran clean in all 60
  tries, and then so did every other trajectory analysis. macOS was not
  affected.

• Water shells use cpptraj's watershell, so waters are placed with periodic
  imaging.

• Pairwise RMSD always asks about subsampling, not only above 500 frames.

• Frame times are never assumed. A file without them used to be treated as
  2 ps per frame.

• Density maps say when the grid limit made the spacing coarser than asked
  for. This used to go to the log only.

• All trajectory-analysis prompt text, choices and option labels are constant
  strings, with no frame counts or residue ranges in them, so a recorded
  analysis replays on any trajectory. The RMSD reference-frame prompt and the
  region menu's "Protein residues" label did not meet this. Session logs of
  these analyses recorded with earlier versions will not replay one to one.

• Contacts, Pairwise RMSD, Water shells and Contact frequency are far faster:
  one vectorised or cpptraj pass rather than a Python loop per atom pair per
  frame.

• The MD Manager's six "Select topology file" prompts no longer carry the
  number of files in their text, so a recorded choice replays in a directory
  with a different number of topologies.

Fixed

• Structure Loader, PDB search results: metals. Search results never carried
  their ligands, organism or chains, because these were read from an RCSB
  record that does not hold them, so the "Must contain metal" filter always
  removed every result. The details now come from RCSB's GraphQL service, in
  one request per 100 structures instead of one per structure, so results
  also appear sooner. With the real components of each entry to work from,
  metals are now read from chemical formulas and no longer from a fixed list
  of eight PDB codes (ZN, FE, CU, ...), which did not know FE2, a heme
  or an iron-sulfur cluster:
  • The results table has a "Metals" column naming the non-polymer components
    that contain a metal: the PDB code, which for an ion carries the deposited
    oxidation state (FE2, FE), with the metal in brackets when the
    component is more than the ion. A nitric oxide synthase reads
    HEM (Fe) ZN. These are the metal-containing components, not the
    residues that coordinate the metal. The column replaces a [Mxn] count
    that was appended to titles, was never explained, and had never been
    displayed.
  • The metal filter takes an element. Fe keeps every structure with iron,
    as an ion under either of its codes or within a heme or a cluster. It
    used to compare what you typed with the PDB code, so Fe found only the
    component named FE. A metal that no result contains is reported,
    together with the metals that are present, and the results are left as
    they were.
  • A metal is any element that is not a nonmetal, metalloid, halogen or
    noble gas. The definition is written that way round so that it cannot go
    out of date: the PDB holds curium, americium and californium ligands
    that no list of metals in ProPrep includes. A metal that is part of the
    polymer chain itself is not reported.
• Structure tables (Structure Viewer and every tool that asks which structure
  to use): after downloading several PDB structures at once, the last one was
  listed twice, so downloading two structures showed three and choosing "all"
  loaded one of them twice. ProPrep keeps the downloaded files in a list and
  also records one of them, the last, as the structure its other tools use;
  the table showed both records. That structure is now listed once, named, and
  marked "current", with a line under the table saying what that means. A
  session recorded with the longer table replays onto the merged row.
• Structure Loader, search results: a structure picked by its row number is
  now recorded with its PDB ID and found again by that ID on replay. The PDB
  grows, so the same search lists the same structure under another number
  later, and a replayed session would have loaded a different structure.
  Selections of several structures at once are still replayed by row number.
• MD Manager trajectory analysis was checked, analysis by analysis, against
  the pytraj API and run end to end on real solvated trajectories, with
  results compared against independent calculations. In 1.20.0 only RMSD,
  RMSF, Ramachandran, hydrogen bonds and radius of gyration ran at all.
  Analyses that failed and now work:
  • PCA, Clustering, Pairwise RMSD, B-factors, Autocorrelation and Contact
    frequency handed the region menu's whole result to the analyzer instead of
    the mask in it. The first four also called the region helper without its
    arguments (_get_analysis_region_selection() missing 2 required positional arguments), and Contact frequency crashed ProPrep outright (a
    segmentation fault inside pytraj). A mask that is not a string is now
    rejected with an error.
  • Nine analyses lost their error message and dropped out of the analysis
    menu with name 'logger' is not defined.
  • Clustering (hierarchical), Water RDF and chi1 dihedrals called pytraj
    functions that do not exist; SASA passed a keyword pytraj does not take;
    DSSP and PCA misread pytraj's return values; Contacts, Salt bridges, Water
    shells, Pairwise RMSD and cluster spreads called pytraj on single frames,
    which carry no topology; Density maps and Vector misread a frame's shape.
  • Line plots, the SASA summary and the Density slice failed in the display
    code once the analysis itself worked, and analyses failed on a trajectory
    that stores no frame times.
• Trajectory analyses that ran but gave wrong results:
  • RMSD, RMSF, PCA and B-factors superposed the shared trajectory in place.
    The periodic box is not rotated with the coordinates, so every later
    analysis that uses imaging (Water RDF, Water shells) changed depending on
    what had been run before it. Nothing moves the loaded trajectory now.
  • RMSD against the "Average structure" was RMSD against the last frame.
  • DSSP on the default C-alpha selection reported everything as coil.
  • PCA "variance explained" was a share of the requested components only, so
    it always summed to 100%. It is now a share of all the motion.
  • Ramachandran paired each residue's phi with its neighbour's psi, averaged
    angles arithmetically (a strand's psi near +/-180 came out near 0), drew
    the plot with its axes swapped, and numbered residues by position.
  • Chi1 and omega results also averaged angles arithmetically, so a trans
    peptide bond fluctuating about +/-180 averaged to about 0 and was counted
    as cis; residues were numbered by position. Both now use circular
    statistics and the real residue numbers.
  • Cluster representative frames were off by one (pytraj reports them
    1-based).
  • B-factors were computed without removing overall tumbling.
• A number typed wrongly at a trajectory-analysis prompt (4,5 for a cutoff)
  was silently replaced by the default in nine places, and crashed out of the
  analysis menu in six others. It is now reported and asked again.
• The Density map grid could exceed its point limit by one along an axis.
• MD Manager "Monitor running simulation" failed with name 'sim_dir' is not defined for every simulation that had data, and repeated the error instead
  of returning to the menu. The Performance Summary and the simulation-type
  check also used re without importing it.
• Structure viewer: the Trajectory panel's "superpose" box scrambled the
  molecule instead of fitting it. NGL (2.3.1 to 2.5.0 at least) copies the raw
  coordinates of each frame into its fit matrix with one index for both the
  3-wide source and the 4-wide destination, so every atom after the first is
  built from pieces of other atoms. With NGL 2.5.0, fitting a rigid, tumbled
  8-atom chain onto itself gave an RMSD of 15.6 A and a 25.6 A "bond"; the
  viewer now applies the fitted matrix itself and gets 0.000 A, and chignolin's
  bonds stay at 1.59 A under superpose.
• Structure viewer: Save Screenshot wrote the default Dark background as nearly
  black, (3,3,3) instead of (30,30,30), because NGL writes an opaque image
  background in linear light. Screenshots and movies are now rendered on a
  transparent background and painted onto the colour shown on screen.

Installers (SHA-256)

Self-contained installers with AmberTools, MODELLER and every dependency; no conda needed. See INSTALL.md.

aec64c9622f44814b6de311af45cf44e5d355d9dd9d2c8a5f7777370e1d4dc13  ProPrep-1.21.0-Linux-x86_64.sh
48ecd7963d795b014a1fa95d6a03f9e125373a59373733fad6b05ce4f7a8293f  ProPrep-1.21.0-MacOSX-arm64.sh
6b7a9aa8f9ab58d23ffcab81ce7df1f13434a274f10e5e5f4e52f391cd0b6ffc  ProPrep-1.21.0-MacOSX-x86_64.sh