We are pleased to announce Coot 1.3:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.3.tar.gz
https://github.com/pemsley/coot/releases/tag/Release-1.3
Paul.
Release Notes for 1.3 Graphics 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 Modelling 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. The conversion uses the Hiranuma inversion: rmsd = 1.5 *
exp(4.0 * (0.7 - pLDDT/100)) B = (8 pi^2 / 3) * rmsd^2 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 Validation 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). This makes it straightforward to flag bonds
and angles whose geometry is statistically unusual, independent of their
absolute size. 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()
Ligands / Lhasa / Layla 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 Maps 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 Scripting and
Automation/MCP 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() User Interface 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 API 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
Build 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
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