
Relase 0.0.33 "Sicilian Rainbow"

Several of these updates were made in Erice (hence "Sicilian")

 o Fix occasional/esoteric crash with Refine Zone on a Water [Joel
   Bard].

 o Checking chiral volumes now gives a result even if not all the
   restraints are found.

 o A new CIF file with restraints now overrides the old one of the
   same monomer name [Charlie Bond].

 o Incorporate code from Kevin to determine the resolution limits for
   map from the available data, not the resolution in the MTZ file
   [EJD].

 o Refmac dictionary reference added to startup text.

 o Homology level for NCS determination exposed at the scripting
   layer.

 o Applied Ezra's map display updates [2-3% speed increase].

 o findwaters improved [Martyn Winn].

 o Find Waters now adds to the water molecule (rather than creating a
   new chain)

 o Cleared up memory leak in bond allocation, I hope [Joel Bard and
   others].

 o "Undo Last Navigation" has a home in the GUI.

 o Update to newest mmdb libs and use the IgnoreHash flag so that Coot
   can read molrep files with # comments.

 o On reading a PDB, Hydrogen names with column 0 numbers are
   corrected according to REFMAC convention.

 o command line program: fix-nomenclature-errors created.

 o Delete Zone reworked.

 o Delete Item now has "Water" entry.  Waters can no longer be deleted
   when "Delete Residue" is active and residues can't be deleted when
   "Delete Water" is active.  This is a good thing and reduces
   mis-clicking [Paul Rowland].

 o Fixed problem of Delete dialog getting stuck in delete-hydrogens
   mode.

 o Symmetry display re-worked.  After superposition, turn off the
   molecule symmetry [EP].  This may affect a few .coot and saved
   sesion files.  The set-show-symmetry function is
   no-longer available, use set-show-symmetry-master instead.

 o Fix a crash when closing the window of a Sequence View of a closed
   molecule.

 o Residue Info reworked.  Now we have a master atom.

 o Changed colours of the model/fit/refine dialog in the cootrc.  I
   did this in Erice (hence "Rainbow").

 o Display Manager reworked.  Now remembers where it was put last
   time, what the size and shape was too.  Also, re-worked to use a
   pane to provide a user-changable divider between molecules and
   maps [FvD].

 o Shelx input considerably re-worked with the assistance of GMS. I
   hope Coot can reaad all shelx ins/res files now - even
   centrosymetric small molecules.

 o Shelx compabibility: .pha files are considered as .phs files.

 o Shelx compabibility: .hat files are considered as .ins files.

 o Mutate Sequence dialog auto fit check-button fixed.

 o Reworked the Go To Atom and other Coordinates Molecules option
   menus.  The Go To Atom option menu should now be consistent with the
   residues tree.

 o Difference Map peaks search now tries to put the peaks around a
   molecule, rather than in the map asymmetric unit [PRE FRS]

 o Bad Chiral Volumes now writes to the console when it can't find the
   restraints for a monomer type [Marianne Cuff].

 o print-sequence and print-sequence-chain write to the console, so
   that now coot can do what pdbset's SEQU SING does.

 o Removed the slow and nearly pointless "Import all Dictionary CIFs"
   from the menu.

 o (Jones) "Rainbow" CA colouring mode.  I decided to add this after
   listening to Alywn at the ACA 2005 Patterson symposium.

 o Included various cleanups from Ezra Peisach.

 o Included multi-molecule bond display speed up from Ezra Peisach.

 o "Missing Atoms" in rotamer analysis are plotted as blue instead of
   red [Qingping Xu].

 o Residues with negative numbers now work in the Go To Atom dialog
   [Qingping Xu].

 o Residue type MSE no longer gives "Missing Atoms" error in Rotamer
   Analysis graph [Juergen Bosch].

 o Rotamer graph now updates on model modification [Juergen Bosch].

 o linkage type between neighbouring and flanking residues now
   dependent on the chem_comp.group value in the restraint for the
   residue types [which means that ligands with C, N atoms and
   consecutive numbering don't get linked and fly away] [Bob Nolte].

 o pick cursor index now changable from the scripting layer [Bob
   Nolte].

 o Rotate/Translate in CA bonds mode moves a CA representation (no
   longer a full atom representation).

 o Resolution limits frame in the MTZ column selection widget now
   under the control of the check button.  This improves the usability
   [EJD].

 o Pointer distances now only displayed to displayed molecules
   [Stephen Graham].

 o Reset View has animated zoom - rather than jump zoom.

 o --auto command line argument for autoreading MTZ files [Randy Read].

 o cis <-> trans conversion [Randy Read, Pierre Rizkallah].

 o user-level hooks available for "." and "," pressed [Charlie Bond].

 o skeleton colouring improved [Stephen Graham].

 o Symmetry control re-worked.  Not it is possible to undisplay
   symmetry of various molecules.  Molecules having undergone SSM
   Superposition no longer have their symmetry displayed by default
   [Ezra Peisach].

 o Change the splash screen.

  

    -------------------------------------------------------
    -------------------- Old Releases ---------------------
    -------------------------------------------------------


Release 0.0.32 "Oranger Hat"

This month, not so much. Been busy with other things as may become
apparent at some stage.  

Anyway, this I am putting out without fully testing, there may be
"funny pick mode" problems - it happened to me once but things got
better using "Clear Pending Picks".

There are several improvements that I don't want to sit on any
longer.


 o Crash on read, close, read, next residue. Fixed.  [Neil Paterson]

 o Animated initial refinement [Kevin]

 o Mutation of nucleic acids [Bill Scott]

 o Change Chain ID GUI [Jan Abendroth]

 o Coot now no longer allows the undoing of changes to a molecule that
   is not displayed [this is not an ideal interface and will be improved
   in future].

 o Fix occasional problem of unreadable MTZ columns [Peter Zwart, Joel
   Bard].

 o Using Ctrl-Z to undo a modification on a second molecule lead to
   problem with subsequently unclickable atoms.  Fixed.

 o Many widgets are now marked as transients (anti-submarined
   (i.e. "stay on top")).  A few of them now remember where they were
   put last time (let me know if there are other dialogs that should
   also be anti-submarined)

 o Multi-model C-alpha mode now available for NMR models [Ezra Peisach]

 o Negative levels in difference maps no longer truncated [Charlie Bond]

 o "Save State" now brings up a fileselection dialog instead of
   writing to an unchangable file name [Dirk Kostrewa]

 o Difference maps read from state file maintain their colour map
   rotation if difference map colours are swapped [Dirk Kostrewa]

 o "Strict NCS" concept added.  The addition of a Strict NCS matrix
   will allow the "expansion" of molecules in the same way that normal
   symmetry does.  Useful for molecules refined with strict NCS in
   CNS (like viruses), I hope (still "in development") [Jonathan
   Grimes/River]

 o "Undo last navigation" bound to "U" key [FvD]

 o Rotate/Translate objects can now be rotated from the keyboard (use
   Ctrl left-mouse and click away from the intermediate atoms) [Artem
   Evdokimov]

 o After Auto-read MTZ, the "scroll" map is the FWT/PHWT map, not the
   difference map [Randy Read]

 o Coot now honours your umask when it creates coot-backup [Gabor
   Bunkoczi]

 o You can turn off the map scrolling by the scroll wheel [Phil Evans]

 o New function to fix nomenclature errors.

 o The top of the Coot's hat on the splashscreen is now more orange -
   less Tajikistan and more India [Neil Paterson].


---

Release 0.0.31 "Anniversary (Indian Hat) Release"

Many of these changes were written during the recent sleepless nights
in Bangalore.  

Coot is officially 1 today... Does that mean we'll get sensible
release numbering..?  Haha not yet!

 o "Scroll" radio button in the Display Manager to ease the changing
   of the scrolling map [at long last, eh Charlie?]

 o Some drawing speed-up code suggested by Mike Hartshorn.  On testing
   I got 40-50% improved frame rates - YMMV.

 o Fit Loop exported to GUI.

 o Now you can undo the deletion of a residue for a molecule that
   contains a single residue [Joel Bard].

 o Reset View on the menubar.

 o Turn off the cell when either its map or molecule are not displayed.

 o Ctrl-Right mouse now does clipping change (up/down) and
   z-translation (left/right) [actually, this is a more or less a
   feature that Frank liked in Pymol and was in the previous
   release too, but I forgot to mention it] [FvD].

 o Symmetry atom pick, now we can pick any symmetry atom (not just
   ones close to the centre) [PRE bug].

 o Don't draw hydrogen atom in the rendered image when they are not
   displayed [Robin Owen].

 o Internal changes so that the 0th molecule can have a colour change
   too.

 o Diagnostic output checking the reference-structures directory at
   start.

 o Fixed some of Ezra's non-initialized variable warnings.

 o guile auxilary code change from guile-www to net-http.  This will
   affect those who compile.  Considerable speed-up in downloading PDB
   files from an OCA server.

 o More status bar messages.

 o Fixed several option menus that didn't alter the molecule that they
   said they would.

 o Fixed crash on multiple deletes then refine zone.

 o Some functions now say in the console what their script version is.
   (print-all-history-in-scheme) gives a history of commands.  The
   coverage is rather spartan at the moment.

 o Lots of documentation updates, now makeinfo is happy.


--

Release 0.0.30 

 Not much this week, I've been ill and have been improving
 documentation.
 
 o Broken hardware stereo fixed.

 o Delete item now move cursor into "pick-cursor" mode

 o Applied torsionable ligand patch from Joel Bard [not the latest
   one]

 o Several internal changes suggested by Ezra Peisach to build with
   sgi CC.


--

Release 0.0.29

This release fixes the botched 0.0.28 version.  There are some feature
requests too.

 o Status bar: has atom pick info and other things [Jan Dohnalek]

 o Now we can colour by molecule too [Andrea Olland]

 o Update go to atom molecule on close molecule [Phil Evans]

 o Measure Torsions [Joel Bard]

 o Use masked map for scoring of orientations in ligand fitting [experimental]

 o Fixed merging molecule chain problems [Harvard oops]

 o Fixed problem of addition pointer atom residue numbers [Wyeth demo oops]

 o Don't write out wiggly ligand models

 o Use group-settings to unset display lists for maps if uname is Linux
   [by popular demand]

 o Add optional atom-based scoring for residue-density-fit

 o new scheme function: fit-protein which does rotamer search and
   refinement for each residue in the molecule.  Sit back with feet and
   and watch the fun job.

 o Use the masked map to score ligand positions rather than the
   unmasked map.

 o Makefile.am fix [Bill Scott]

 o configure.in fix [Ezra Peisach]

 o Documentation updates (including the F8 key).

--

Coot-0.0.28 release notes

This is a bug-fix release with a few feature requests added.

 o A crash and generally woolly thinking has been fixed in the Align &
   Mutate function

 o After a chat with Martin Noble, display lists have (optionally)
   been added for maps.  It is not clear if this will help on your
   hardware - for me, it makes my PC worse but my Mac faster.  This
   may address the concerns of Phil Evans and Andrea Schmidt.
   Map display lists are on by default.  To turn it off:
   (set-display-lists-for-maps 0)

 o Delete Item on a symmetry related item now deletes the real item
   (and consequently symmetry copies).

 o Flexible ligands are now pre-regularized (anti-bumped) after
   torsion angle manipulation

 o Chi Angles for MSE fixed [Marianne Cuff/Phil Evans]

 o Chi Angles values displayed [Dirk Kostrewa]

 o New function: de-clash (see documentation) for de-clashing
   sidechains without a map [Kay Diederichs] (Clashing waters can be
   deleted with the validation water checker).

 o Cancel on the Map Colour Selector actually cancels the colour
   selection and takes you back to the colour you first started with
   (instead of doing nothing) [Many people doing the tutorial at
   Grenoble found this one]

 o NCS sequence comparison improved [Adrian Lapthorn].

 o Water searching now tells us the distance parameters it is using.

 o Delete Item now has a checkbutton to keep the dialog alive [Adrian
   Lapthorn]

 o Fix SSM configuration problem [Joseph Toth]

 o Double-click during Refinement gives 2 "Accept Refinement?"
   dialogs.  Fixed. [EJD]

 o Density fit for residue now auto-updates on accepting refined
   residues

 o Various internal updates to make Windows port easier

 o Various documentation updates

   I had been having problems keeping the documentation
   in order - but now I think that the manual will appear spookily up
   to date.

--


coot-0.0.27 has been released.

Fixes issues raised by Kate Kavanagh (alignment and mutate chain
problems), Adrian Lapthorn (coloured intermediate atoms), Ian Tickle
(brief atom labels), Marianne Cuff (water/ligand addition problems).


--

coot-0.0.26

I made an important oversight in 0.0.25.  The ccp4mg utils function
Tree used in chi angles and rotamers was modified and I forgot to
update one of its uses (the rotamers).

So I am releasing 0.0.26 as a fix.

On the plus side, this version has a couple of other fixes and has a
least squares interface and shelx interface that are getting released
sooner than I had planned (these aren't documented in the web pdf
manual yet).

--

0.0.25 has been released.

Updates include:

o fixed crash on .phs data but no symmetry for molecules

o fixed N-terminal add terminal residue crash

o fixed crash on rot/trans of alt-conf selection [thanks Stephen Graham]

o Added chain chooser to SSM superposition

o Fixed symmetry atom picking (which sometimes gave spurious hits)

o more annotation for SSM overlapping results (work still to be done
  here, thanks for testing: MOL)

o NCS tool: Edit -> Bond Parameters now has NCS "ghosts" available for
  display (overlay B chain on A chain)

    e.g. http://www.ysbl.york.ac.uk/~emsley/coot/screenshots/coot-ncs-ghosts.png
    The result of a chat with Charlie Bond at Galashiels

o NCS tool: Calculate -> NCS maps: i.e. e.g. overlay map for molecule
  B on molecule A. Does averaging also.

o Fixed various Makefile.am problems [thanks Joseph Toth]

o Real Space Refinement of Water atom now available (it actually does
  a rigid body fit)

o Pointer distances (distances to the pointer - so that you don't have
  to add an atom to a structure before you know the distance of a blob
  centre to the protein atoms)

o Various fixes trying to get rid of accidental "Translate Only" mode

o Delete atoms from the structure "on top" when multiple structures
  overlaid (more work to be done here it's still too easy to
  accidently delete stuff "at the back")

o Fixed occasional problem with MTZ column label checking

o "Filename filter always on" option (needs more intricate widget work)

o moved from COOT_RESOURCES to COOT_PIXMAP (coot will have icons one day)

o fixed occasional discrepancy between the bond parameter molecule
  option menu and the molecule of the bond parameter options

o fixed python function state naming problem [thanks Bernhard]

o Water masking is no longer optional in water search [forced on].  No
  longer possible to put waters on top of existing waters

o Water checker validation tool now available [about 10 months after
  Florence asked for it]

o Experimental "Align and Mutate" feature for Molecular Replacement models

o Option to allow the swapping of colours after refmac (so that the
  new map has the same colour as the pre-refmac map

o difference maps are now by default shown after running refmac

o Tassos encourages the use of "Real Space Refinement" label

o Clicking on "RS Refine Zone" while the delete window is open no
  longer deletes the residue

o Turn off skeletons properly now

o Rendered images now contain balls (as well as sticks)

o In Ca-mode, Coot no longer "runs out of colours" past the 8th chain

o Several corrections to enable compilation without the GSL (but not
  recommended)

o Fix typo in contouring algorithm that occasionally deleted a
  contouring line [thanks Ezra]

o Bond parameters dialog now has slider for colour map rotation - much
  better than text entry

o Fixed "No solvent" view atom indexing problems [thanks Ward Smith]

o Fixed the mask inversion, so we can easily make nice piccies like this:
  http://www.ysbl.york.ac.uk/~emsley/coot/screenshots/coot-mask-raster3d.png

o Now using newest CCP4mg code for atom tree (ligand chi angles).
  Note that the tree is built using the clicked atom as its base -
  this is still under development (I'm not happy with it) but may
  improve things

o I'd had a few reports that there were gaps when using Ca Zone ->
  Mainchain. So I tinkered with a couple of filtering parameters -
  lets see how it goes...

o citation banner enabled [the Coot paper has been published - yey!].
  Splash screen amended too


--

coot-0.0.24 has been released.

o Added IRIX case to setup scripts and added COOT_REF_STRUCTS.
  Hopefully that'll put these problems to bed.

o Check the bonds type before making bonds after setting hydrogen bond
  drawing state (Charlie Bond's bug)

o Calphas + Ligands in Sec. Struct. colouring now works (ditto)

o Added a few GUI warnings as per Ezra's suggestion

o Go To Atom widget residue tree improved

o Fixed-up ligand searching dialog - no longer crashes at execute time
  when no ligands found.  Re-worked so that the searching dialog doesn't
  appear unless there are ligands available.

o Re-write of map colour selection and scroll-wheel attachment code.
  Now the maps are enumerated and one doesn't get the option of
  changing the colour of closed maps

o COOT_SCHEME_DIR and hard-wired default directory searching logic
  change

o insertion code support for Go To atom: now Coot displays the
  insertion code in the (graphics) atom label and in the Go To Atom
  residue tree item labels and double clicking on such a thing goes to
  the right residue (you still can't refine it when you get there
  however)

o one can no longer add Pointer Atoms to closed molecules

o Refmac running extra parameters code cleaned up

o Downloaded files go now to directory coot-download, not .coot

o MSE standard residue more sensible now (apparent after mutate
  residue to MSE)

o Substantial re-write of atom naming code in dictionary reading.
  Still not all correct yet but better than it was - it may even be
  faster to generate the geometric validation graph.  Coot can now
  refine NAD and MSE (MSE chi angles still fails).


