
Tue 28 Feb 15:54:45 GMT 2023

   From 8th Feb
   add hydrogens atoms, auto-fit rotamer -> messes up bonding  ::: 2


Thu 23 Mar 15:45:49 GMT 2023

    - sequence mismatches ::: 2

    - B-factor this vs average/sd B-factor environment ::: 2

Fri  7 Apr 03:52:28 BST 2023

   - make an interface to gaussian surface that allows me to specify the atom selection
     (e.g "all atoms", or "not ligand")  ::: 2


Tue 18 Apr 23:04:19 BST 2023

   o Add Bond-by-distance (normal/basic coot bonding)  ::: 4

Mon 24 Apr 23:06:48 BST 2023

   B602 ZN is normal atom size in 4puc (so it looks tiny compared to the water atoms) ::: 1

Mon 24 Apr 23:13:58 BST 2023

   Filo ligand indexing problem:
   
   https://app.pumble.com/workspace/640ef18548ea1715f1efcfd7/6410560e58fdda5cb73d0199?message=6446c12b9d80c05aa5a8ff56

   ::: 2

Mon 24 Apr 23:16:03 BST 2023

   Make the GM restraints drawable - use generic-3d lines?

   ::: 1

Mon 24 Apr 23:32:59 BST 2023

   for the agenda: middle-mouse for panning.


Fri 19 May 17:40:33 BST 2023

   A check for git server,
   B check how much pyrogen is transferable

Fri  2 Jun 16:02:06 BST 2023

   o function for fix atom at position (and refine for n cycles)

Sat  3 Jun 19:33:43 BST 2023

   o in coot-refinement we have move_single_atom_of_moving_atoms(). That doesn't care if the
     atom has been marked fixed or not!


Thu  8 Jun 05:49:47 BST 2023

    From molecule_class_info_residues.cc

   // Lovell et al. 2003, 50, 437 Protein Structure, Function and Genetics values:
   // BL says:: should these be the one set?!
   //ftype level_prefered = 0.02;
   //ftype level_allowed = 0.002;

   ftype level_prefered = graphics_info_t::rama_level_prefered;
   ftype level_allowed = graphics_info_t::rama_level_allowed;


Wed 23 Aug 16:04:12 BST 2023

   Add a std::string message to simple-mesh.hh so that when the status is 0, then an error
   message can be displayed. For example selecting //A/1-111 in 1x8b.
   Gaussian surface on //A/901 doesn't work either.



--- Done Items ---

   o add a status flag to simple_mesh_t - used for "did we run out of memory/bad alloc"? (say) ::: 1
* Done.

