Release 1.1.20

Release Notes for 1.1.20

o FEATURE: "New Residue Type" now available in Add Other
Solvents dialog.

o FEATURE: key-binding for Triple-Refine AA (H)

o FEATURE: key-binding for Undo Symmetry View (Shift V)

o FEATURE: key-binding for Keyboard Mutate (Shift-M)

o FEATURE: now Open Dialogs track the latest used directory

o FEATURE: "Unhappy Atom" markup added

o FEATURE: Add keyboard mutate

o FEATURE: on initial startup, Coot will ask if left-mouse
should be used for view rotation

o FEATURE: (Multi) Pick Delete Atom added

o FEATURE: Bad Non-bonded contact markers now have dashed lines
between the atoms

o FEATURE: The space group info is now displayed in log on reading
a coordinates file

o FEATURE: Now configuration with --sound works

o FEATURE: Other types of Carbohydrate added (back)

o FEATURE: server mode turned into JSON RPC server

o CHANGE: XDG is used for the download of COD entries

o CHANGE: Update the "No Unmodelled Blobs" dialog

o CHANGE: Update the url for AlphaFold models to v6

o CHANGE: User-feedback when trying to rotate unselected chi angle
improved

o CHANGE: Cross-hairs have fixed size, not relative size - the
size is configurable in Preferences

o CHANGE: "Environment Distances" is now a transient [Oliver Clarke]

o CHANGE: CA Label now follow the residue on "Space" repositioning

o CHANGE: Recentre on new fragment on "Copy Fragment"

o CHANGE: Overlay notification on B-factor and Occupancy updated

o CHANGE: B-factor and Occupancy modification now has an overlay
notifier

o BUG-FIX: "Undo molecule" dialog operation fixed

o BUG-FIX: Display Control dialog is only displayed on restart
if it was displayed on session save

o BUG-FIX: fix control of display control dialog in the
state script

o BUG-FIX: fix missing protein-ligand interactions for FLEV
[thanks Lan Guan]

o BUG-FIX: set_molecule_name() function for models fixed

o BUG-FIX: one can now no longer pick/drag undisplayed intermediate
hydrogen atoms [thanks Oliver Clarke]

o BUG-FIX: the "No Unmodelled blobs" dialog tided up

o BUG-FIX: get-monomer dialog activate now closes the drop-down.

o BUG-FIX: undisplay "Get monomer" frame on entry activate

Chapi/libcootapi

o NEW FUNCTION: get_mmrrcc()

o NEW FUNCTION: get_residue_pucker_info() function added

Release 1.1.19

o FEATURE: Double click to label symmetry atom

o FEATURE: drag-and-drop import for local-file-system files

o CHANGE: user-defined-clicks function added back

o CHANGE: Assign and Associate Sequence menu item functions now added back

o CHANGE: Improve the scrolling of the map contour level when the
nominated map is not displayed

o BUG-FIX: Menu items with targets don't work on macOS (I don't know why)
The targets have been removed, so these menu items should now
work again (e.g. Fetch and Mutate menu items)

Release 1.1.18

Release Notes for 1.1.18

• FEATURE: Ctrl-F keybinding added to smooth the bonds
• FEATURE: Multi-select for opening maps
• FEATURE: "Side-chain 180°" button now does syn/anti flip for nucleotides
• FEATURE: "Split Water" added to Modelling menu
• CHANGE: "Copy Fragment" has become an overlay
• CHANGE: "Move Molecule Here" has become an overlay
• CHANGE: Generic Display Objects can now have translation gizmos
• CHANGE: layla now has relocatable directory support
• CHANGE: Monomer-library look-up reworked
• BUG-FIX: Removed bug in parsing external torsion restraints
• BUG-FIX: Curlew has moved to use XDG Base Directory specs

Chapi/libcootapi:

• CHANGE: the way the monomer library is looked up is improved
• CHANGE: get atom and get residue functions are now available in nanobindings
• CHANGE: swig has been removed from pythonic api
• CHANGE: format() function added for residue and atom specs

Release 1.1.17-v2

This is the same as 1.1.17, but has updated/corrected ChangeLog and coot.appdata.xml.

Release 1.1.17

Release Notes for 1.1.17

o BUG-FIX: Save symmetry coordinates is fixed

o BUG-FIX: Colour-by-B-factor colours are fixed

o BUG-FIX: Place atom at pointer fixed

o BUG-FIX: Optional Gemmi usage restored

Release-1.1.16

Release Notes for 1.1.16

o FEATURE: Local B-factor display

o FEATURE: Built-in logging (started) - view it by clicking the "Log" button

o FEATURE: Full doxygen documentation transfered to chapi nanobind functions

o FEATURE: Anisotropic probability radius scaling (thank ClAuS Flensburg)

o CHANGE: For packagers: Now a commonly-used fragment of the monomer library
is bundled with Coot. Unknown monomers are now downloaded from GitHub
and cached using XDG Base Directory Specification

o CHANGE: For packagers: Now the reference structures are bundled
with the source code (and installed) - no longer do they need
to be a separate dependency

o CHANGE: If a map has a PANDDA:: or APPLY-SYMMETRY:: label then Coot now
properly handles that (turns off "is-EM-map" status)

o CHANGE: Atoms with Zero Occupancy results now moved into the
main window

o CHANGE: Boron atoms are now pinky-beige - like Jmol

o BUG-FIX: Fix crash on adding an atom [Clément Bousquet]

o BUG-FIX: Symmetry atoms are now clickable for distances and labels

o BUG-FIX: Fix the non-drawn clashes post model update

o BUG-FIX: "Add Other Solvent Molecules" dialog has been depythonized
and now will work on macOS

o BUG-FIX: "Copy Molecule" dialog has been depythonized and is now an
overlay and now will work on macOS

o BUG-FIX: Fix the problem of focus-grab when using Tutorial Model & Data

o BUG-FIX: Fix the "Close" button in the Restraints Editor

o KNOWN-BUGS: (that I looked at at but don't know how to resolve):
- Ramachandran plot on macOS
- Menu items that use targets on macOS
(I suspect OpenGL driver bugs and GLib problems on macOS)

Release 1.1.15

Mostly a bug-fix release, although I did manage to squeeze in feature - drag and drop now works.

• FEATURE: Drag and drop (partial - it works from the file browser,
  but not from CCP4i2)

• FEATURE: set_use_vertex_gradients_for_map_normals() added to the Coot API

• CHANGE: Fixed atoms are now draggable

• CHANGE: max-closeness is no longer used to filter peaks in map_peaks_py()

• CHANGE: Backtick for selection now also shows the residue range (if set)

• BUG-FIX: Track-pad zooming fixed

• BUG-FIX: Residue Info dialog buttons now on the right hand side

• BUG-FIX: Fix and Unfix atom now work as expected

• BUG-FIX: Remove erroneous "No ligands Found" dialog when ligand fitting

• BUG-FIX: Select Map for Fitting dialog now behaves has expected on reopen

• BUG-FIX: Merge Molecules dialog now behaves has expected on reopen

• BUG-FIX: Choose a better contour level for masked maps

Release-1.1.14

o FEATURE: Clark&Labute-like 2D-ligand environment view in Coot,
Moorhen and chapi

o FEATURE: Symmetry represented as solid model (no longer just lines)

o FEATURE: PAE Plots on downloading Alphafold models

o FEATURE: new chapi functions:

is_nucleic_acid()
delete_all_carbohydrate()

o FEATURE: Setting the primary mouse button for view rotation enables
secondary mouse button for zoom (like Old Coot)

o CHANGE: chapi modules name now changed to coot_headless_api
so that the molecules_container object can be called
chapi

o CHANGE: Alphafold downloads are now XDG Base Directory compliant

o BUG-FIX: NCS-jumping has been fixed - Bernhard Lohkamp

o BUG-FIX: unwritable XDG cache dir now longer causes a crash
[Jordan Dialpuri]

o BUG-FIX: Shader for drawing ribbons

o BUG-FIX: About and Preferences dialogs can now be properly closed.

o BUG-FIX: Texture handling for bad NBC markers updated [Fixes crash]

Release 1.1.12

Release 1.1.12

o TERMINAL OUTPUT: Coot's startup, in particular the graphics and Python, have
lately been problematic (i.e. flaky/broken). Different operating systems,
different drivers, and different versions of Python add to the complexity.
We have spent quite some time refactoring this - and especially so in the
last few weeks. To help understand what is going wrong on startup I have
increased the amount of diagnostic information on the terminal - so it's a
bit ugly at the moment.
When issues have been resolved and the startup is stable, I will reduce/remove
the diagnostics.

o FEATURE: new chapi functions:

add_terminal_residue_directly()
copy_molecule()
flood()
get_validation_vs_dictionary_for_selection()
servalcat_refine_xray()
get_torsion()
change_alt_locs()
split_residue_using_map()
get_missing_residue_ranges()
get_mutation_info()
set_temperature_factor_using_cid()
Pythonic API:
   https://www.mrc-lmb.cam.ac.uk/lucrezia/libcootapi-documentation/api.html
C++ API:
   https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/api/html/

o FEATURE: New Coot API functions:

set_new_non_drawn_bonds()
add_new_non_draw_bonds()

o FEATURE: Added graphics viewport scaling

o FEATURE: Added Acedrg link interface

o FEATURE: HOLE interface has been restored

o FEATURE: Transform map by LSQ model fit has been restored

o BUG-FIX: --code now works again after XDG Directory Protocol
update

o BUG-FIX: Fix the use of the no-recentre-view in coordinate file open dialog

o BUG-FIX: Contact dots for ligands now show ligand donor to water H-bonds

o BUG-FIX: One can no longer refine using a CCD dictionary [Lorenzo Masso]

o BUG-FIX: Use the correct shader for surfaces in "Plain" mode

o BUG-FIX: LSQ Fit dialog now works

o BUG-FIX: CYS with hydrogen atoms no longer try to make SS bonds
[Jordan Dialpuri]

o BUG-FIX: End-of-chain TER atom now removed on adding a new terminal residue

o BUG-FIX: Dark mode icons now work in Layla

o BUG-FIX: Use a wider window on startup on macOS

o BUG-FIX: Global Phasing column labels F_early-late now auto-read

o BUG-FIX: Delete Hydrogen atom in Layla now works

o CHANGE: Remove/reduce framebuffer usage in --opengl-es mode

o CHANGE: Module menus depthonized

o CHANGE: Overlay added for Cryo-EM "Flip Hand" tool

o CHANGE: Pythonic start-up has been changed - hopefully improved

o KNOWN-BUGS: Ramachandran Plot display on (some?) macOS