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-*-text-*-
EDS:
ebi.ac.uk/pdbe/entry-files/*.mdb
to be updated
scripts rev 5732 (some prodrg stuff needs testing) generic objects, update running of jligand?! (r4782, need to use gtk.gdk.pixbuf_new_from_file() then) , check_ligand.py is dummy dict-gen for windows...
check drugbox in python
tests rev 5460 update
build-it-win rev 4739 (check 0.8 pre builder, add publishing?!)
missing script:
ligand_check.py
run_mogul.py
ligand_check_refmac_columns in enhanced_ligand.py
enhanced_ligand.py test it
Dictionaries:
KCX, TPP
-------------------------------------------------------
* THINGS TO DO BEFORE 0.8.1 RELEASE * ONLY URGENT THING
-------------------------------------------------------
Fix a preferences dir function (in graphics-info already)
Make requirement for probe/reduce more obvious, i.e. give better error message
and better info in installer (which no one reads).
Aniso not working on windows machines 0.8.8 (incl build machine) was ok 0.8.2
rev 5761 (ok on my machine too) => check libraries
New Rama: drag residues->switch to selection and rather refine (e.g. add
extra torsion to ref target)?!
check up to dateness of supplied manuals
Windows bat use %~dp0 to replace coot prefix and fiddling with installer files
Windows bat use %~dp0 to replace coot prefix and fiddling with installer files
refinement selection with insertion code not working
Fix installer guile warning for windows feel.
-- before 0.8
Windows:
o replace msys with HOME in wincoot build scripts
o in general make wincoot build more general/compatible
o check installer on win 8 (hangs after finished)
o distribute src code!!!
o change runwincoot.bat to (win)coot.bat
o write things to WINDIR (rather than HOME)
o check if clipper::ClipperInstantiator::instance().destroy(); is still needed in c-interface-gui.cc
o try (again) using backward.cpp
---- FINISH URGENT ----
Tsukuba 2014:
- toolbuttons (or such - combobox/menu?) to switch on/off helix/strand restraints
* Done, but missing integration
- DB loop for guile -> activate?!
- BUG (?):dock sequence window stuck at ~ 7 sequences - maybe not, but not scrollable
BioCrys 2012:
- sequencing GUI: give more approriate error messages, e.g. if chain
id is missing
- preferences of older Coot versions may not be compatible with newer ones.
Maybe only try to import, to avoid crashes!
- Tutorial 2:
o try to move baton building to later
o update position of baton build (other modelling tools or such)
CCP4 APS 2012:
- GUI for patterson (Garib)
CCP4 SW:
- seq vs PIR have extra button to insert, delete, mutate
- Windows: save working dir directory to properties/start in (possible?)
- powerpoint plug in
- show all bond distances (angles etc?) for ligand/residue
- update WIKI (key bindings)
OIST-CCP4
- indicate rotamer option somewhere/how [PhilE]
- delete/hide DB loop candidates after accepting?!
- stereo: shift/shear rather than rotate [PhilE]
- brightness warning dialog behind other dialog-> move forward?!
- change occ for master (accept return or just tick button)
- after change the canvas (geometry) doesnt work for non-aa any more
- improve seq assignment interface (take all seq, assign to all prot chains etc)
- seq alignment produces N-term gaps which are not there... (gap to -2.5?)
...and some other in seqeuence strangeness, need to adjust gap parameters
.. maybe alignment parameters should be cutsomisable....
APS 2011(?)
- copy NCS (chain and residue range) to specific chains (not just all)
- wider range for B sharpening (est. from Wilson?! determine cf Bruenger?) - needed?
- automatically adjust NCS matrix type (i.e. fast for larger mols/more ncs)
- backrub selection in refinement selection dialog
-
CCP4
- baton build no chainid (?)
- 2nd baton build 'overrides' 1st
notes from BioCrys
- correct resno bsed on associated sequence (note: associate sequence produces
nonsens gaps at ends)
- associate sequence GUI result GUI buttons, have action too rather than only
go-to-atom (have pair of buttons)
notes APS CCP4 workshop
- document refmac extra params + lib files location (note to self ?!)
scripting exercise
- shortcut for setting 0, 1, 0.5 occupancy
- extend helix
- adjust alt conf/occupancy
- variance test for aa
- doublicate residue range with alt conf
----------------
* TO DO THINGS *
----------------
**** General ****
o allow export of goograph points (and/or draw these separately after
passing of parameters)
o revisit (re)move TER when adding a C-terminal residue
o revisit anti-aliasing. Seems we need to antialias before drawing map
and lines and not in general, I think.
o fix intelligent_previous_atom in molecule-class-info.cc when going
between chains, e.g. 1mru. Actually a problem forward too [MW]
o place waters based on two maps e.g. both 2FoFc and FoFc
o better error messages when ccp4 (e.g. libcheck) is not available
o do clash checking on symmetry interfaces
o user defined click shoudl stay cross haired as long as there is
clicks pending (count the clicks?!)
o function: make atom ANISO B
o add atom info to HETATM info in status bar!?
o revisit B-factor setting for new atoms. Still CB wrong when stubbing.
maybe set new B to overall B from mol (rather than default!?)
o renumber residue should not allow doublication of residue numbers
o keyboard shortcut letters for mutate?!
o proper sphere selection (without neighbouring crap) and keeping
of all specs (and alt confs) - use double mmdb selection method
from Eugene
o add more things to Preferences, e.g. no of auto refine residues steps;
add nomenclature error check to preferences
reorienting_next_residue
Preferences could include all (almost) default
settings from globjects e.g.
add zero occ box size??
set_default_initial_contour_level_for_map
set_label_on_recentre_flag(state)
set_draw_cis_peptide_markups(0)
o make auto_read column labels public and expandable (cf pdb, mtz extension
list)
o Edit chi angles crahes in no-graphics mode
o user defined click should keep selecting mouse pointer
o desensitise refmac buttons etc if no ccp4/refmac installed
o add (more sensible) timeout for download at EDS (and others?)
o optional: do not increment file save no/automatically overwrite (dangerous)
o torsion angle refinement:
- shrink atom ardii or downweight nonbonded
- use phenix updated torsion library
o add most common ligands to find?!
o views play is not interuptable?!
o check that labels cannot be set to black accidentally/reset
o colour/display residue/ligand by distortion score (like mogul) but based
on dictionary (better than nothing!)
o backup file does not change name when saved in between (Feature/bug?)
o Additional representations need tree and/or other better navigation
o Additional representations/ballNstick tick marks do not update with
Clear Ball and Stick
o Water validation tick partial occupancy removes most other waters too
o Check NCS copy when insertions etc. May need update of matrix
and/or use of SSM rather than LSQ. Mmh. Tricky
o save screenshot (and maybe other figures - or else) doesnt have a
root directory to save in set (in file chooser)
o NCS not always identified properly (e.g. 3c10)
(ERROR:: An NCS reference chain finding error has occured)
o Edit phi/psi shown appropriate rama underneath
o Kleywegt plot shouldnt be sensitive to non-displayed residues
o validation (and similar) graphs shoudl be aligned
o Cys in symmetry looses SG
o raster3d: water as sphere, include labels, make surfaces, comment in code
o ligand searching: split in smaller fragments then torsion search and/or
use fragment for partial disordered ligand
o change chain ID: automatically check overlap (plus warning)
o mutate all Met->Mse
o refinement with non-bonded terms: select larger area for non-bonded only
o shift sequence/insert residue (for out-of-register errors)
o turn off backup before phosphorylation
o include gsl.h (or such) in gsl config test
o edit charge of ions (atoms)
o List of residues (e.g. alt conf) maybe display res type too
o extend alt conf from side chain to whole (and vv)
o EDS needs better error/fail handling!
o ..same for get from pdbe (when no or bad cif, e.g. 2MBR)
o Ca->main Chain for whole chain (not just zone)
o give warning (dialog) when trying to make a main chain from less
than 6 CA
o display python/guile info in about dialog
* Done (may be done nice?!)
o fix icons for CENTOS, Red hat etc. (replace with fixed_icons.tgz?)
o pisa: - H-bonds always displayed
- ignores alt-conf for H-bonds (gives warning in get atom spec)
- works only for v 1.13 and above (python)
- use qtpisa?!
o accept_regularizement does not effect the gui(s ?)
o add term residue in radius around?
o give sequence view window a title (and maybe many more...).
o reset (cap) ANISO
o change kleywegt chains in plot
(only display single chains in Ramachandran - same dropdown?!)
o print Ramachandran outliers
o set_go_to_atom_chain_residue_atom_name (and maybe others, for sure 'space')
do not update environment distances
o cancel plane picking!!!
o Validation summary
o graphical ssm/lsq output
o read pdb string
o fix modal show_select_map_dialog in all instances!!
o 'map_scroll_button_2' widget not found (display manager warning)
o update sequence view after rename and renumber chains/residues
o gradually include residues for refinement, good if completely out
(maybe not)!?
o check for updates in About?! Include info on pre- or release!?
o phs file dialog, make fill/expand properly
* Done (quick fix)
o domain NCS (use parrot's code?!)
o make LINK search and LINK in pdb
o seq view colour by alignment (optional/button)
o Go to Atom does not update when open and new molecule gets created
o delete chain (model) function (in scripting I guess)
o pick pointer disappears when using delete hydrogens (maybe in others too)
when keeping dialog open
o show symmetry axis !?
o grab focus of loaded state file window (only Win?)
o recalculate NCS
o 'force' NCS on non-matching sequences (*done?!)
o validate on top waters (already done maybe in 0.7)
from Osaka 2010
o add preferences, dock accept refine etc in tutorial!?
o fix atoms dont give traffic lights (bug?)
o toolbar for other modelling tools?
o (more) menu separators (?)
o remove model fit refine dialog (for gtk2?)?
-
o symmetry phosphates of DNA are bonded and not (i.e. get cross)
o what about ONLY torsion angle restraints for low res?
o add solvent molecule creates new monomers every time, check for existing ones
o space bar kills density fit window; feature or bug
o Difference map peaks do not respond to . , shortcuts
o symmetry colour button doesnt update (needs proper colour button)
o enable Alt key for scripting keyboard shortcuts
o water check for B below threshold?!
o Tooltips for residues in new sequence view?! (wait for goocanvas - has
build-in tooltip)
o Edit Chi for hydrogens not working (H from reduce at least)
o transform whole asu for packing comparision?! (check mmdb, use ORIGX?)
o doublication of find strand/find ss (Extensions, Other tools)
o glycosylate residue
04/11/08 CCP4 dev meeting:
o activate bulk solvent correction for refmac?
o filechooser in save mode doesnt have delete & rename file!? Shall/can we?!
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 ?!
04/10/08
o simultaneous refinement of alt confs
o interface to thomas schneider superposition program (ESCET)
o rigid body fit per residues (* done? bb script?! No! extend to nulceotides
i.e. use sugar and base as rb)
o fix OXT refinement
(maybe not now, as it may be fixed with MODRES etc... certainly already better)
o density histogram graph?!
o calculate/display skew of map
o additional representations: hide parts of model (use bond thickness 0?!?
bond thickness 0 doesnt work. hiding seems tricky!?
o povray view angle still not ok (view gets smaller the further away from
origin we are) use openGL matrices?!
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 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 How about interfacing to a Wii?
o tutorial/documentation for scripting/extensions [Ronan Keegan]
o high resolution auto-build
14/08/08
o probe dots on selected residue range (Bob van Dreele)
o move (& merge) symmetry related molecules (globularize?) Done?
16/09/08
o 'new', short display manager
22/09/08
o notes to self:
- ribbons: include ribbons
save the ribbons for later use (?, maybe better to update and generate new)
sort out colouring
get lighting sorted
use CMMDBManager somehow...
- ccp4mg ellipsoids
low importance
* add rcrane reference
**** Python ****
o keep refmac pid to cancel and kill refmac in download pdbe
o get recent ebi skip queue and timeout if 404 return (esp for pics
which are not there - any more)
o make some menu items in extension radio menu items, e.g. NCS matrix,
rotamers - there may be more
o make coot_gui into a method?! Maybe resolves some issue, e.g. loosing entry
o (toggle)toolbuttons for secondary structure restraints
o simple script to insert residue
o if there is no python scripting. Dont load python scripts etc.
o add other solvent molecule -> dont import cif again?!
o residue type selection convert to upper case (maybe best a combobox)
o db loop fit does not delete residues if going back to original loop. Not
trivial, since replace coords or copying keeps the last added ones.
o find_exe/command_in_path
- more generic with respect to extensions (Win mainly)
- take all drive letters (Win only)
- move graphics in right place
* Done (mostly), could expand on the graphics part and add a file storage
for found/defined exes
o export COOT_PYTHON_DIR
* Done? but useful? CHECK
o make variables e.g. ROTAMERSEARCHMODE... work to be set
not possible I think. Cannot overload function/variable in python
could use lower case function!? May be confusing...
o streamline generic_entry functions, one generic one should be enough!
o associate sequence: tick box for all chains
o List of 3d annotations e.g. for delete
o make rotamer and auto-zone fit protein function!?
o slider to change stereo angle factor (and add toolbutton for it)
o cootaneer shows 2 sequences after only 1 has been assigned before?!
no map selection possible
o find below occ 1 atoms (not just zero).
o make a quick test (no 3 x ramachandran)
o find close atoms (on top waters)
o residues with missing atoms gives empty dialog, better give info_dialog
o tooltips for flips/clashes molprobity
o fix os.path arguments to be string (e.g. normpath)
o user_defined_restraints: rename and fix old RNA names
o use shell_command_to_string where possible
o change title in progress bars to % when downloading!?
o get ebi latest: use some queueing! server limits requestes?!
o remove probe dots if interactive probe is toggled off (???)
o merge ligand chains?!
o extensions menus separators (fill in)
o enable PISA interface for new enough PISA
o rethink threading - maybe better integration in event loop possible?
o check output libraries/cifs from libcheck, esp from smiles
o update documentation (tags); make extra file with title?!
o different 'Control_' spellings in key board shortcuts
o make all 'macros' (e.g. with_auto_accept) to use all sort of input
(list, args, ... - cf using_active_atom)
o refmac warning when no freeR (how to detect?!)
o document remote connection
o make a server-client swapped version for remote control (if possible)
o fix 'No Adjustment' buttons (and callbacks) in user_mods_gui
(*done?)
o review pygtk button (and other) callbacks which are string, poss can be
exchanged (see water_coordination_gui)
o fix addition of guile and python keybindings (translation of lambda functions?)
o key code for '(' and ')' not recognised (on FC10 e.g.)
o update python WIKI scripts
o fix guile translator, seems broken (or not, find a good example, seems ok)
o python: rapper-gui and what-check (*Done?!)
o make guile-gtk properly gtk2 complient (esp. text-view) or wait for
proper gnome-guile
**** Windows ****
o write a log to file (and maybe error too).
o pass args from msi to exe
o make real msi at some point
o distribute probe and reduce (from Richardsons? if not ccp4)
o make batch msi (using msiwrapperbatch and config file)
o fix runwincoot.bat when PYTHONPATH points to a pygtk installation.
o 64 bit windows version
o Add Documents\ and Settings//My Documents to favourites in filechooser
o build script: better for pango's friends (output and check)
o fix dragNdrop for filenames with spaces!!
* Done for main window - still needed for Lidia!
o write proper path in state file if file is absolute (i.e. include drive letter)
o fix find-ligand (and maybe others) for use in Windows. Arg parsing not
working on MinGW (maybe DOS?)
o write some info in registry to see that WinCoot is actually installed
together with version info install dir etc maybe; ask for uninstall
these.
o make install syminfo.lib from windows dir
o use fftw binaries
o write installer to registry/installed programs etc.
o load pdb problem with space and/or umlaut in path!?
o new gtk chooser sometimes only displaysrecent files rather than all
save state
save symmetry (even small)
o use CCP4s lib dir rather than REF_DIR!?
o ccp4 project dir not showing up (with new gtk2 chooser)
o pop up dialog if disk space is limited!!
o installer: show/hide details
o fix DATADIR objidl.h conflict
o windows not reading gz file if space in name
o optionally include reduce/probe (via download?)
o update gtk!?
o test srs
o Test spider drag and drop (not working on windows - broken gtk)
o distribute srces!!
o make installer log
o installer options for guile/windowsy (sections)
* Done (although now vs vs)
o installer option to install (or not) icons/shortcuts
o use dlls in rdkit/enterprise rather than static ?!
o set sbase dir (maybe)
o make clean before new stable release! check and uninstall old python!?
o update download in defined directory, may go into examples folder
o streamline installer dirs/files, install and remove (use /r)
o swap guile and windows section in installer
o enable guile with extra warning in installer
* Done, but better warning required!
o update with guile?
o changed runwincoot->wincoot.bat; make compatible
o investigate gtkglext stuff for newer gtk
o make a second test for windows?!
o move from runwincoot.bat to coot.bat and include in svn
o check that update mechanism works with windowsy feeling
o replace $COOT_HOME with %HOMEDRIVE%%HOMEPATH% or %APPDATA% or ??? ?
o installer with custom/typical to make easier (use InstType)
o check save times with gz compression, maybe make optional (feels slow)
(* Done - optional compress that is, make entry in preferences?)
o better python std flushing for MINGW
o update WinCoot to guile 1.8.6 (if possible)
o simple guile implementation in WinCoot
o windows build: dont update src tar whilst building (if possible)
o merge build-it-win with build-it-gtk2-simple?!
o A comprehensive 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
**** Ribbons ****
o fix colouring for electrostatic surface -> should use fractional
o put old ribbons code in branch
o fix str char warnings
o change name of functions (check with Paul)
**** Tutorial ****
o include Sphere refinement
**** general ideas things to test ****
o solvent region noise estimation (sigma/abs)
o 2nd derivative maps! (usefull?)
**** dynarama ****
o give phi-psi info in tooltip (maybe optional)
o close menu could be "quit" in stand alone
o (better) exception handling when e.g. no glade file
o add function for user to show selection of res only
o 2nd residue in kleywegt should get green box too (or not)
o add setting for chains when using a selection in kleywegt
o shades between the favoured-allowed-disallowed
o selector for multiple models
o add torsion angles for interactive movement
o drag residues->switch to selection and rather refine (e.g. add
extra torsion to ref target)?!
o compare rama by mol choose A and A and show appropirately in selector
(see first topic)?!
o wrap kleywegt arrows different in reverse order (e.g. tutorial-modern.pdb
B->A gets long arrows)
o make psi range option -120->240 (optional)
* Done
o contour lines thinner (?) and black
* Done
o play with colours?!
* Done(ish)
o kleywegt is not applied when open a new molecule
* Done
o fix green box position
* Done
o stand alone: change pos of green box too.
* Done (?)
o stand alone works without arg and we can load a molecule with open?!
* Done
o when use open, set title and stats
* Done
---------------
* DONE THINGS *
---------------
o labelling with 'l' doesnt show status bar info (feature/bug?)
* Done
o fix using_active_atom with respect to lists
.. and extra args
* Done
o add read_vu files for python
* Done
o move mol here: should auto display molecule!?
* Done
o docked toolbar disappears when return is pressed
* Done
o toolbuttons for probe dots chi and post-refine
* Done
o make toogle_toolbuttons
* Done
o optional tooltips for main toolbar buttons
* Done
Osaka 2010
o fix size of chooser dialog (if possible, gtk2 bug?!)
* Done (appeared to have been a gtk2 bug)
o replace os.system with subprocess
* Done (maybe kill needs a revisit)
o save state cannot be expanded (as chooser?!)
* Done
o rainbow doesnt ignore water (if in same chain)?!
* Done
o fix atoms dont have pick cursor
* Done
o sphere_refine_plus, i.e. sphere_refine with extra residues
* Done
o reset Ramachandran lights in docked accept/reject dialog
* Done
o do not create .coot-preferences if not needed?!
* Done
o undocked refinement toolbar always on top
* Doneish (bug on Windows and maybe other systems)
o refinement toolbar R/RC and Map should expand in text mode
* Done
o bond colours dialog: remove(hide) general setting as already in preferences
* Done
o add no map wheel rotation to preferences
* Done
o separator after built-in toolbar buttons
* Done
o grey out python/scheme when not available as scripting window
* Done
o fix new large icon size for search water, preferences model toolbar (there
may be others)
* Done
o rework coot_python
* Done
o replace tooltips with tooltip (for newer pygtk)
* Done
o update build-it
* Done!?
o update python 7z install (only for pygtk, newer ones have msi!)
* Done
o update gtk (and gtk-glext)
* Done (stupid gtk 2.16/gtkglext problem, newer version of gtk dont work
with gtkglext, not even the git one -> investigate!!!)
o martyn mrc ccp4 lib stuff in windows build
* Done
o update windows to guile gui
* Done
o update windows to new(er) RDKit (incl assignRadicals etc)
* Done
o Esc removes docked acccept/reject toolbar
* Done!?
o Windows NCS skip: after new chain(?), doesnt work, need to jump out of new chain (e.g. water)
* Done
o WINDOWS:: update mechanism for stable release uses pre-release dir! Grrr
* Done
o WinCoot:
- update gtk? Better for Windows 7?!
- before stable release copy python over
- silent python installation? Possible? (http://www.autoitscript.com/autoit3/)
* Done
o icon on WinCoot website
* Done
o label main Window WinCoot
* Done
o preferencable main toolbar
* Done
o update statusbar using space skipping
* Done
o disable the 'Question Accept..' in Preferences
* Done
o check Win7 installation bat file mod [Jola]
* Done
o phs read on windows convert slash [AT]
* Done
o sort python text completion in scripting entry
* Done
o FIX pythonic probe/reduce status (seems ok at the moment?!)
* Done
o check recovery (once nomenclature is fixed)
* Done
o increase icon size
* Done
o SSM of copied fragment doesnt work
* Done
o jligand/names/path in CCP4 vs website
* Done
o libpng patching (properly)
* Done
o full screen mode? maximize screen function!?
* Done