 -*-text-*-

scripts      rev 2902 
tests        rev 2893
build-it-win rev 2122

---------------
* THINGS TO DO BEFORE 0.6.2 RELEASE *
---------------

   o update Windows, check up to date in pending-install dir!?

   o review pygtk button (and other) callbacks which are string, poss can be exchanged (see water_coordination_gui)

   o transform whole asu for packing comparision?!

   o better python std flushing for MINGW

   o doublication of find strand/find ss (Extensions, Other tools)

   o make md5sum note on WinCoot website

   o optional tooltips for main toolbar buttons

   o DNA/RNA backbone is not displayed for symmetry (CA mode)

   o glycosylate residue

   o update WinCoot to guile 1.8.6 (if possible)

   o fix addition of guile and python keybindings (translation of lambda functions?)

   o key code for '(' and ')' not recognised (on FC10 e.g.)

   o website guile comment

* Done

   o simple guile implementation in WinCoot

   o update python WIKI scripts

   o labelling with 'l' doesnt show status bar info (feature/bug?)

   o WinCoot:
        - update dictionaries!!
* Done
	- update to python 2.6 (now with pygtk etc)
* Done
	- before stable release copy python over
	- silent python installation? Possible? (http://www.autoitscript.com/autoit3/)

04/09/08
   o loop building backwards in scheme (use python?)?

* Done?!

22/12/08
   o fat bonds remain after ball-n-stick from additional repr (TS)
* dont understand (seems ok to me)

   o notes to self:
     - ribbons: include ribbons
  		save the ribbons for later use (?, maybe better to update and generate new)
		sort out colouring
		sort out licence (add to svn and commit) test dist first
		use CMMDBManager somehow...

   o windows build: dont update src tar whilst building (if possible)

04/11/08 CCP4 dev meeting:
   o bulk solvent correction for refmac?

   o filechooser in save mode doesnt have delete & rename file!? Shall/can we?!

   o windows test system:	- start XP for testing after installer build
				- install WinCoot silent
				- download test data and unittests
				- run tests
				- send email about status/or notify otherwise

---------------
* TO DO THINGS *
---------------

   o refinement weighting by occupancy

   o running shelx should be 'threaded'

   o add all GtkWidget and similar functions as ignore to coot.i (script)

   o simulate middle mouse with Alt left ?!

   o revisit refinement convergence of alt conf refinement

   o update WinCoot to guile 1.8.6 (if possible; not yet).  [PE Note: try 1.9?] 
                                                            [BL tried a while ago but not successfull]

   o ccp4mg ellipsoids

   o interface to thomas schneider superposition program

   o rigid body fit per residues

   o fix OXT refinement
     (maybe not now, as it may be fixed with MODRES etc... certainly already better)

   o density histogram graph?!

   o additional representations: hide parts of model (use bond thickness 0?!?
	bond thickness 0 doesnt work. hiding seems tricky!?

   o revisit python sockets

* Done?!

   o merge build-it-win with buid-it-gtk2-simple?!

   o test vista compositing (* Done?!?!)

   o povray view angle still not ok (view gets smaller the further away from 
	 origin we are)

   o refmac to run from an XML file

   o read_refmac_log to read refmac XML output (if there)

   o use libglade

   o cootaneering (more testing, make documentation?)

   o alternatives for loop building (wait for Kevin's implementation)

   o add terminal residue (if Gly, Pro) use different target ramachandran
	 function for placement of term residue;
	 maybe we want to try general rama first, then Pro, then Gly (if we 
	 dont know the residue type) for better loop fit (or in general)
	 this may require some Gly noise filtering as Gly always will fit best

   o side chain treatment in low res maps (test if torsion angle restraints 
	 are good enough) otherwise we may want different weight for MC and SC
	 and/or B-factor refinement

   o fragment fitting/search

   o rsync builds to Paul's dir

   o How about interfacing to a Wii?

   o "Check for updates" button? (need to know which OS we are on, maybe 
     from the install dir?!)

   o read_shelx ins file:
	 does it remove comments correctly? (! comment) from line!!!!

   o tutorial/documentation for scripting/extensions [Ronan Keegan]

   o python: rapper-gui and what-check (*Done?!)

   o high resolution auto-build

14/08/08
   o probe dots on selected residue range (Bob van Dreele)

14/08/08 
   o change orientation of refinement toolbar and make it dockable to 
     other sides of main window

* Done (but not automatically to change orientation)

14/08/08
    o make guile-gtk properly gtk2 complient (esp. text-view)

29/08/08
	o refinement of H at high resolution blows H around (fixed?)
	
	o move (& merge) symmetry related molecules (globularize?)

	o pictures in manual (how and where!?) Maybe more extensive (advanced)
	  tutorial!?

10/09/08
   o no bond colours if no element column in pdb file (e.g. CNS files)
     try to guess?! use coordconv?? new mmdb should fix

16/09/08
   o 'new', short display manager

22/09/08
   o fix size of chooser dialog (if possible, gtk2 bug?!)

04/10/08
   o simultaneous refinement of alt confs

06/11/08
   o individual runwincoot.bat for multiuser WinCoot installation [Neer Asherie]

---------------
* DONE THINGS *
---------------

   o new options for recentre in gtk2 file chooser - combobox (and extensions - radiobuttons)

* Done 

19/01/09

   o stereo/mono button for side-by-side stereo [Victor Alves]

* Done

   o antialiasing in s-b-s stereo only left panel (bg colour messed up too) [Victor Alvez, me]

* Done

   o Display Manager position setting not reliable (same for Go to Atom - fixed?!)?! [Victor Alves]

* Done

15/01/09
   o update Refmac GUI SAD as in new CCP4i

* Done

   o after associated sequence no sequ input in fit loop

* Done 

   o fix returned lists in coot_gui.py combobox fillers

* Done

   o merge solvent chains [JG]

* Done

   o test and implement user defined func python

* Done

   o fix pass-build/pass-test (with guile build) and include progress status

* Done

   o separate test sets when running one test set

* Done

   o 17/12/08: set difference map doesnt do 'nice' default difference map colours [Jodie Guy]

* Done

   o antialias depending on bg colour

* Done

   o torsion general 'Reverse button' for docked accept/refine dialog

* Done

   o fix toolbuttons (upon loading with 'new' python import module)

* Done

   o test for add_residue not giving 'real' atoms

* Done 

   o coot.in to be MinGW compatible

* Done

   o website guile comment

* Done

   o interuptable refinement in python

* Done

   o include density-score-by-residue.exe in WinCoot installer

* Done

   o build-info: show pass-build but dont make installer if test fails (WinCoot)

* Done

   o annotations in Extensions

* Done

   o (scripting) GUI to find zero occ atoms.

* Done 

   o spawn refmac and use timer to get progress rather than blocking
     the application; maybe plus kill button?! NEEDS guile version

* Done (python)

   o fix addition of guile and python keybindings (translation of lambda functions?)

* Done

   o key code for ( and ) not recognised (on FC10 e.g.)

* Done

   o fix zalman command line switch

* Done

   o simplify Windows installer script (use /r)

* Done

   o fix threading in python 'Coot News'

* Done

   o stop tests when problem loading modules

* Done

   o in INstaller SetOutPath before FINISH_PAGE_RUN (but where? test!?)

* Done

   o Uninstall properly based on all/single user (SetShellVarContext)

* Done

   o fix python ebi download

* Done

   o tutorial data in share/coot/data for WinCoot !?

* Done

   o FIX PNG suport for Windows!!!! Bad Paule!!!! Grrrr

* Done

   o Installer needs to set affinity for Windows 7 too?!? (OrIf, WindowsName = 7)

* Done

   o add the binary_type_latest to the WinCoot installer script 

     [And the rest of the phone home system: updates are available?
     download, install, restart (just like firefox) - 20090711-PE OK,
     it's not sensible to schedule this for 0.6.]

* Done

   o fix toolbuttons (upon loading with 'new' python import module)

* Done

