
--- Items ---

o Let's move the light for different shadows in Fancy Mode

o make "Environment Distances" an overlay

o make downloading emd map an overlay

o Ctrl-M should merge molecule (active ligand) into other model

o fix relocatable instation of coot-residue-density-fit.
  See the homebrew install.

o put contact dots on the residues around the ligand.
  How about hexagonal slabs (instead of balls) as
  an option? (Tricky to get the orientation correct "between" atoms).

o pickable ribbons.
  Big Job.

o double-click on a symmetry atom to label.

o does get_ligand_validation_vs_dictionary() do good things?
  Does it give ceus?

o Bonds and angles validation on 2d diagram from chapi
  as svg.

o arwen, alejandro, santosh, dorothee

o check for g.display_control_window() usage - they should
  not be needed these days, I think.

o have another look at the PAE drag box for residue selection

o Take a cif molecule, copy it, move the copy to symmetry-related position
  merge with first and write out the cif. Is the header (secondary structure)
  preserved in the outpute cif?

o Robbie: 3pdt is Mg and should be K. A2.

o moorhen (and coot) ribbon diagram coloured by b-factor

o read in a molecule, make a molecule with DNA models. Refine DNA, then
  try to undo refinement of DNA. Fails. 8v1w.

o check that hydrogen bonds are displayed correctly.
  See update_hydrogen_bond_mesh()

o fix the map caps. Make it work in moorhen. Single colour mode and joined edges.
  Slice "solid" maps.

--- Other Items ---

o "Flood the blob with dummy atoms" - useful of pomgnt2

o Add ability to rotate view around z axis :: 0.5

o auto-scale the make-a-difference map
  think about create power-matched option also? It's in chapi :: 1

o colour stops for b-factor analysis, rather than colour wheel. :: 1

o have another look at Rama plot :: 1

o Add curl fetch stuff to chapi api. Use modern accession codes.

o address-sanitizer for coot

o Fix the "Fetch" buttons - new GTK4/glib? :: 2

o "Proportional editing" molecule rotation :: 2
  Actually "fragment" rotation makes more sense.

o Get in touch with Kay for the display of h,k,l as atoms (cif)
* Done. Progress has been made.

o Atom sphere radius depends on B-factor - proportional to cube root maybe?
  set_atom_radius_by_b_factor_mode(imol, state)
  atom_radius_by_b_factor_scale_factor(imol, sf)

o draw 9c1h with molecular symmetry colouring :: 1
  turn on set_colour_by_ncs_chain(imol, 1)

o "Proportional editing" molecule rotation :: 2
  Actually "fragment" rotation makes more sense.

o try texture atlas for text - make a new test app from scratch :: 4

o WTA carbohydrate :: 6

o what does "RenameVerticesAndTriangles()" do? Do we need it?

o Cross-out "Screenshot" unless we have OpenGL 4.2 or later :: 0.5

o Highlight the chain neighbours in the Rama plot. Bring back the green square.

o how do I make the HUD buttons have rounded edges? Can I make the health bars
  have rounded edges?

o Rama and Rota graphs validation graphs have terrible scaling - difficult to fix :: 4

o Have a look at contact dots during refinement - with the 3a3a say, there is hang, and the
  final refined structure is shown - there is no animation :: 2

o Have a look at the poly-TRP problem of sequence identification. :: 4

o  It was a strange bit of code in get_group().
   Now the issue is duplication of the model on writing. mmdb bug.
   Solved now? Am I using the right version?

--- Done Items ---

o make "Copy Fragment" an overlay
* Done.

o get rid of generic object functions from graphics-info.h
  Put them in aa new file along with
  bool is_valid_generic_display_object_number(int obj_no) const;
* Done

o add header guard to gizmo and gensurf headers
* Done.

o change stringify_error_message to stringify_error_code
* Done

o rename Cartesian.h to Cartesian.hh
* Done.

o Move Molecule Here should be an overlay
* Done.

o Talk to Stuart:
::function get_atom not found - out of 386 docstrings
::function get_atom_using_cid not found - out of 386 docstrings
::function get_residue not found - out of 386 docstrings
::function get_residue_using_cid not found - out of 386 docstrings
* Done

o Move Molecule Here should be an overlay
* Done

o move make_directory_maybe() to take std::string arg.
  Will need to change the header. Maybe a new header?
* Done.

o side-chain 180 should do a syn/anti flip for nucleotide bases
  i.e. rotate 180 around C1-N1 (or N9)
  Make a video. In chapi too?

o what are the chi angles for ASN? In sequons? With link
  to NAG?
* for Lucrezia. Use top 3000 filtering on modern structures to
  get new reference set.

o User-defined filename filter for coords file open
  https://docs.gtk.org/gtk4/class.FileFilter.html
* Assigned to Jakub

o make a file that maps CCD-id to RDKit Canonical SMILES.
  (is the SMILES in Acedrg output the canonical SMILES?)
* Looks good. Jakub to continue this

o Add split water to new coot
* Done.

o install latest chapi, python3 import coot_headless_api
  then the molecules_container_t gives an error message
  about COOT_PREFIX
* Not for me.

o std::bad_alloc when fitting waters in chapi - maybe.
  Put some protection in.
* Done.

o filename filter for coords file open
  https://docs.gtk.org/gtk4/class.FileFilter.html
  Done. But now I think that this is not what Oli wanted.
  There should be a user-defined globbing string.
  Add a GtkFileDialog to a dialog. See google docs notes.

o multi-select for maps
* Done

o 2vf7: alphafold model tutorial? Or is it too close to the actual model?
  *It's too close.  Good idea though.

o bernie comments
* Done.

o refine_residue_using_cid "CHAIN": too much debugging information
* Done.

o Fix curlew (download to wrong directory)
* Done.

o make a function that returns the secondary structure for libcootapi/chapi
* Done.

o print the key bindings
* Done.

o add-water should have a key-binding
* Done.

o swig should not be a dependency if building chapi
* Done. And done.

o Process Stuart's outliers file ::: 1
* Done

o fix the colour wheel in B-factor analysis ::: 1
  1geh B-factor colour ramp looks wrong

o Add Metals to Coot startup, Moorhen and chapi ::: 0.2
* Done.

o Save symmetry coordinates.
* Done

o what is the radius of gyration? Make a function. ::: 1
* Done.

o remove GEMMI hack at top of atom-selection-container.cc ::: 0.2

o make a function that returns the secondary structure for libcootapi/chapi
* Done

o key-binding for smooth bonds
* Done.

o layla needs a wrapper and to be moved to libexec
* Done.

o get rid of debugging on get_h_bonds()
* Done. Nice.

o move make_directory_maybe() to take std::string arg.
  Will need to change the header. Maybe a new header?
* Done.

