o FEATURE: Map caps ("sliced apple" view): a 2D coloured cross-section of the electron density on a clipping plane, stitched seamlessly to the trimmed 3D isosurface behind the plane: add_density_map_cap()
o CHANGE: MoleculesToTriangles meshes now use material-based lighting
o CHANGE: Default material tweaked: ambient raised from 0.1 to 0.2 and diffuse lowered from 1.0 to 0.5, giving softer highlights and less blown-out surfaces for objects that don't set their own material
o CHANGE: Improved depth-of-field shader
o CHANGE: Reworked depth fogging in the moleculestotriangles shader; objects drawn with draw_meshed_generic_display_object_meshes() now also use depth fogging
o BUG-FIX: Fix the colour rotation of the difference map negative level
o BUG-FIX: Fix the residue-number colour ramp for colorRampChainsScheme: the ramp range now uses only amino-acid residues (waters and other heteros were skewing the min/max), each chain gets its own ramp colour scheme, and the HSV saturation is bumped from 0.4 to 0.6 for more vivid rainbow chains. Problem seen in 4zzn.
o BUG-FIX: Screenshot resolution now uses framebuffer_scale instead of a hardcoded 2x
o FEATURE: "Symmetry as C-alphas" button added to the Coot: Symmetry dialog
o CHANGE: Atom labelling reworked so that it happens on mouse button up
o BUG-FIX: Fix the rotation jump after zooming
o BUG-FIX: Fix scaling and offsets in graphics_ligand_mesh_molecule_t::draw()
o BUG-FIX: Fix the NCS jumping centre
o FEATURE: Molecular Placement for cryo-EM maps
o FEATURE: hiranuma_inversion() added - converts the pLDDT scores (0-100 confidence values) that AlphaFold stores in the B-factor column of its predicted models into physically meaningful isotropic B-factors, so that AlphaFold models can be used with refinement, density-scoring and validation tools that expect real B-factors
o BUG-FIX: Fix action mutate_base_to_type_U name
o BUG-FIX: Restraints lock now acquired when updating NBCs in minimize()
o BUG-FIX: Atom indexing error fixed in update_extra_restraints_representation_geman_mcclure()
o BUG-FIX: For ramp_chains, the polymer range is now known
o FEATURE: "Proportional editing" rotation added
o FEATURE: Delete symmetry waters from the rotation centre
o BUG-FIX: Fix behaviour of the residue range selection in renumber residue range
o BUG-FIX: Fixups for environment distances
o FEATURE: NCS validation graph enabled
o CHANGE: distortion_bond_mini_stats() and distortion_angle_mini_stats() now also calculate nZ, the normalised z-score of the deviation from the target value (deviation / sigma)
o FEATURE: Current-residue marker added to the Ramachandran plot
o CHANGE: Density correlation validation graph sped up
o CHANGE: Pucker analysis geometry fixed up
o BUG-FIX: Close the validation Ramachandran box when a molecule is closed; refresh_ramachandran_plot_model_list() now called in close_molecule()
o CHANGE: Drug fetch now uses ChEMBL instead of DrugBank (DrugBank is blocked by Cloudflare)
o FEATURE: Lhasa extended IO: import and export for various data formats
o FEATURE: Lhasa can now read and write RDKit pickles
o CHANGE: FLEV SVG output now has width and height before the viewBox
o CHANGE: Compile guards so Lhasa/Layla still compile when RDKit has no Coordgen support
o BUG-FIX: Fix rotation and overall jankiness in coordgen mode
o BUG-FIX: coordgen error no longer printed when there is no coordgen support in RDKit
o FEATURE: Browser for new ligands added
o CHANGE: recent_new_ligands.py reworked to use the new PDBe API
o BUG-FIX: Fix the inner ring bond positioning
o FEATURE: Functions added to control the lighting of maps
o FEATURE: brighten_maps() added to the Coot API
o CHANGE: EMDB map download reworked: now uses an in-window progress bar; recentre message no longer shown for map download; download-emdb-map-label is no longer used in fetch_emdb_map()
o CHANGE: Reading a map again moves to the middle of the box
o BUG-FIX: Fix the download directory for maps
o FEATURE: Cmd++ to increase the font size in the virtual terminal
o FEATURE: VTE terminal as a replacement for the Python entry, with coot_vte_repl.py
o FEATURE: Servalcat outliers JSON input (servalcat_outliers_json_for_coot.py)
o BUG-FIX: Prevent double-running of startup scripts
o CHANGE: new_startup functions renamed to startup
o FEATURE: --dictionary-with-mol added to the command-line options
o BUG-FIX: Re-enable command line scripts in run_command_line_scripts_callback()
o FEATURE: Aniso and H-atom filtering in the Save Coordinates dialog
o FEATURE: "Edit -> Residue info": "Apply occupancy to atom with alt conformation" checkbox restored
o FEATURE: "NCS Ligands" user interface added
o BUG-FIX: Fix crash in display control delete button
o BUG-FIX: Widget protection in on_display_control_delete_molecule_button_clicked()
o BUG-FIX: Fix TER atom counting in AMBER trajectory processing [eunos-1128]
o BUG-FIX: Fix names of the entries in the NCS ligands frame
o FEATURE: GUI item added for "Sort Chains"
o FEATURE: Residue info shown in the status bar when hovering over circles in the Ramachandran plot
o FEATURE: Atom Overlaps display now controlled via a toolbar toggle button; "Delete All Generic Display Objects" now correctly prevents overlaps from reappearing after refinement
o FEATURE: "Local B-factors" now activates display immediately when the menu item is clicked
o FEATURE: GUI control for map generic objects added
o CHANGE: Validation graph correlation colours reworked: more red at mid-range values, muted professional colour palette
o BUG-FIX: Fix the alt conf occupancy slider in the rotamer dialog after "Add Alt Conf": the slider now has an adjustment, draw_value, marks at 0.0/0.5/0.99, and 0.01 step granularity
o BUG-FIX: Fix "Go To Atom" dialog raising from the macOS Dock
o BUG-FIX: Validation graphs now updated after side-chain 180 flip and peptide flip
o BUG-FIX: "Add OXT" now respects the current bonding mode
o BUG-FIX: Fix duplicate entries in the "Add OXT" molecule combobox when reused
o BUG-FIX: Fix the sequence view to extend to the end of the residue range (ligands and waters were being clipped)
o FEATURE: Active residue is now highlighted in the sequence view; sequence view is now updated on model modification
o FEATURE: add_picked_atom_info_to_status_bar() added
o CHANGE: Molecular representation's mesh_vbox is now inside a GtkScrolledWindow
o CHANGE: Clear Atom labels item moved
o BUG-FIX: Stop picking of symmetry atoms when symmetry is not displayed
o BUG-FIX: Fix the active item of refinement control comboboxes
o BUG-FIX: Close the side panel when the difference map peaks box is closed
o BUG-FIX: Fix drag-and-drop file dropping
o FEATURE: rebox_map() and apply_translation_to_molecule()
o FEATURE: get_map_cap_mesh() on molecule_t and molecules_container_t, for headless map cap rendering
o FEATURE: delete_links_containing_residue_py() added
o FEATURE: to_generic_object_add_tori() added
o CHANGE: render function made const
o BUG-FIX: Check for LIBRSVG version before using rsvg_handle_render_cairo()
o BUG-FIX: Fix backward.hpp for PowerPC
o CHANGE: Eigen3 is now required at configure time
o CHANGE: GSL autobuild install now links against libcblas so that libgsl.so carries DT_NEEDED libcblas (or libgslcblas) which eliminates the --as-needed cblas_* undefined-reference failure
o BUG-FIX: Use CMake for RDKit in Lhasa; pre-install Eigen for Lhasa
o BUG-FIX: Fix nanobind resolution for venvs
o BUG-FIX: Fix nanobind find_package broken without -Dnanobind_DIR
o BUG-FIX: Fix linking of maeparser and libexpat
o BUG-FIX: Fix non-/usr-based Chapi build
o CHANGE: Removed --with-enhanced-ligand-tools from coot configure
o CHANGE: maeparser and coordgen added to build-it-3-3; eigen updated to 5.0.1

Coot

Install on Linux