
------

    Release 0.4, Dec 2007


   o Richardson rotamers

   o Try again to add chiral volumes to the geometry target function

   o Add Chiral centre inversion and cis peptide generation check 
     after refinement or regularization.

   o Make the Omega Angle Plot update properly

   o Add Chiral Volume Outliers to Omega Angle Plot

   o Post-install slim the binaries

   o Do the strand restraints work well under refinement?
  
   o Add planar peptide restraints as default

   o Add atom selection by sphere 

   o Add map masking by variable radius about atom (selection)

   o Cootaneer

   o Activate test suite

   o Faster bonding of multiple models e.g. 1O5P.pdb.  It should take
     1 or 2 seconds.


-----

   Release 0.5 Dec - estimated for 15 August 2008.

   o To make the test non-tedious, especially on slow computers, we
     need a set-atoms-attributes that takes a list of attribute sets.
     No need to re-calulate the bonding for each atom move.
     No need to redraw, except once at the end.

   o Make a new dialog: clear up old/backup files on exit.
     86400 seconds per day

   o Kleywegt plot should not draw ("wrapped") long arrows

   o Torsion General

   o Lars Prade crash.  Try doing actions in a directory that you can't
     write to.  Test Geometry validation.

   o work in the svn-revision.cc.  svn-revision.cc should be in
     Makefile.am, and be part of the tar file.  It should be generated
     after every time we do a svn update or commit.

   o On pressing the filter button we get this ugliness:

** (lt-coot-real:8759): WARNING **: Widget not found: coords_fileselection1

** (lt-coot-real:8759): WARNING **: Widget not found: dataset_fileselection1

** (lt-coot-real:8759): WARNING **: Widget not found: coords_fileselection1

** (lt-coot-real:8759): WARNING **: Widget not found: dataset_fileselection1

     on_filename_filter_toggle_button_toggled() looks up the
     fileselection by going through all names of file selections. This
     is ugly (gives terminal warnings).  Make the user data also encode 
     information about which fileselection this is (in 1000s, say).

   o Dynamic distances on moving atom/fragments

   o Make build-it-gtk2 and use it.

   o Correct CISPEP if needed cards on writing pdb.

   o Mutate should not change the order of the atoms in the pdb.
     http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html

   o Fix this:  
      ./configure: line 26927: ./po/POTFILES.in: No such file or directory
      (it comes from building from the tar file)

   o Kevin's Ramachandran Refinement target

   o Use Eugene's new LINK-reading code.

   o Fix Charlie Bond's shelx ins writing bug ("shelx woe", 10 sept 2007)

   o Valgrind long/multiple fit-proteins

   o "Thick bonds" for ligands etc

   o Insertion codes for intelligent next atom

   o Add some SHELX reading to the test suite.  Insulin for starters.
     Check that the space groups agree.

   o graphics::molecules should be a std::vector

   o Copy fragment (new-molecule-by-atom-selection) does not
     recalculate the NCS.  It should.

   o test/fix hardware stereo in Gtk2 mode.  Also side-by-side  
     problem described (for example) by Randy Read.

   o NCS Ligands: if we find a ligand C in molecule A, we should look
     for a similar blob near molecule B and try to fit the same kind of
     ligand there as well [JED]

   o If we have guile scripting in configure, then we should check for
     net-http and goosh have been installed.  If not, fail gracefully,
     not obscurely at run time!  
     net-http and goosh to go into Coot directly?  Maybe not, the get 
     installed in a different place.  Hmm.

   o The default occupancy for new atoms in a shelx molecule should be
     11.0.  Is it? [JED]

   o How about a post-swig command to add #ifdef USE_PYTHON around 
     coot_wrap_python.cc (or is it coot_wrap_python_pre.cc?)

   o Check Richardson Rotatmer library is correctly used for GLN, ASN, PRO.
     Ask about Rotamer misses.  Well, the dictionary is fine. Why does
     molprobity web site gives less bad rotamers then? (First: Does it?).
     Yes it does: e.g. for 1sar molprobity notes only these:
     "Bad rotamer B  47 GLN (0.3%)" 
     "Bad rotamer A  91 LEU (0.4%)" 
     "Bad rotamer A  13 PRO (0.9%)" 
     "Bad rotamer B  41 GLU (0.7%)" 

     There are 10 times more for Coot.  
     (fix-nomenclature-errors doesn't fix anything)

   o NCS differences graph (use master chain)

