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|
-*-text-*-
---------------
* TO DO THINGS *
---------------
o additional representations: hide parts of model (use bond thickness 0?!?
o revisit python sockets
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 ribbons from aesop python things from CCP4MG (at some point)
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 fix threading in python 'Coot News'
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 make coot icons anti-alias
* Done
o fit_gap in both direction => dialog to select A or B
* Done
o auto-mutate after add terminal residue with sequence
* Done
o find 32/64 bit povray exe (WinCoot) [Yen-Chywan]
* Done
o python's read_refmac_log to run after schemey refmac run
(if we have pygtk)?
* Done
o schemey run-refmac to work with twinning/sad etc.
* Done (testing?!)
o python: rapper-gui and what-check
* Done (what_check)
o switch on/off refine toolbar (preferences)
* Done
o option for toolbar on the left (preferences)
* Done
o fix the alignment of icons and labels in the Model/fit/refine dialog
* Done
27/08/08
o make example keybindings for python (based on Paul's scheme bindgs)
* Done (put on Kay's WIKI)
27/08/08
o Windows installer:
- question overwriting of runwincoot.bat
- make the 'start in' directory user changeable (use SetOutPath!?)
* for both make sure it works (sensibly) with a silent installer!!!
* Done
04/09/08
o check licence header in python(-test) modules
* Done
o test db-main strands windows fix thingy (debackslash)
* Fixed
09/09/08
o check key binding codes for () []
* Fixed by using gdk keymapping
o replace popen and spawn in python with subprocess functions!
* Done
o clean-up use of probe/reduce command_name and command (python)
* Done
22/09/08
o current directory in chooser shortcuts
* Done
o update tutorial with preferences
* Done
07/10/08
o make pygtk gtk1 compliant (incl import gobject test)
* Done (well not compliant but shouldnt crash)
15/10/08
o make loading svg (in absence of libsvg) fail save
* Fixed
22/10/08
o add missing Model/Fit/Refine buttons to modelling toolbar (if possible)
- Torsion General
* Done
15/10/08
Notes from Phenix
o readline not accessible with ftp but with http in build-it-gtk2-simple?!
may just be temporarily?!
* Done, server was temporarily down
o compile without GSL fails in graphics-info.hh as redefinition of
refinement_results_t -> check (remove in graphics-info.hh?!?)
* Done, compile without gsl now (not sure how usefull and if as functional as possible)
o update the tutorial with Kevin's figures?!
* Done
o add copy button to LSQ fit
* Done
o always be able to use mtz file in Refmac GUI
* Done
o clean up the build-info webpage files/dirs for WinCoot
* Done
o reset B-factors of refined/changed atoms
* Done
23/10/08
o sync MFR dialog with modelling toolbar -> all or selected for toolbar
* Done
o make all modelling toolbar icons preference-able
* Done
o update probe/reduce to work with pdb v3 (remove oldpdb)
* Done
o update WinCoot website for new probe/reduce use
* Done
o clean-up use of probe/reduce command_name and command (python):
actually should not delete and overwrite group_settings.py
upon installation, in case people change the name of probe/reduce here.
* Done
22/09/08
o current directory in chooser shortcuts
* Done
o read refmac log for outliers in Extensions
* Done
o notes to self:
- backup windows imgs
- revise script to delete older binaries.
* Done
o colouring/highlighting in console output in Dos Shell
* Done
o set_display_lists... for windows stereo
* Done
o zip/unzip pdb backup files in windows
* Done (use gzip)
o dont use TLS in refmac if we dont have the button (i.e. new refmac)
* Done
o Ramachandran restraints check button for loop fit
* Done
o do loop building 1/2 from N and 1/2 from C terminus for langer loops (>=6?)
* Done
04/10/08
o make toolbutton GUI/wizard
* Done (check which ones to use!?!)
30/10/08
o LSQ option for ncs copy residue range
* Done
o clean up Windows code:
- warnings about V_UNKNOWN
- clean up the windows magic jiggery
* Done
o Preferences -> default -> apply font colours
* Done
|
