18 months after the release of Coot 1 it's time for Coot 1.1
Coot 1.1 is a major change beyond Coot 1. It has required a lot of
writing and rewriting and has been the focus of my work since last year.
Technically (but briefly) we have rewritten the GUI again so that it is
now is based on GTK4 (Coot 1 used GTK3). This has meant a lot of rewiring
under the hood so that things behave similar to before [1].
Many things, that is. Not all things. There are a few important
differences - they are for the better (although you may not initially
think so).
o View rotation is on right-mouse (except on Mac).
o Functions are activate in "Select First" mode (that means bringing
the atom/residue/chain of interest to the centre of the screen)
and then choosing the function. This is more consistent with the
use of hot-key/key-bindings.
o Widget "focus" is different in GTK4 - I don't yet fully understand it
at the moment, so, in case Coot "forgets" to revert focus back to the
main graphics widget, there is a "Grab Focus" button in the horizontal
toolbar.
o Many of the menu items have been moved around. Now they are far more
likely to be where they will finally end up.
o "Modelling" (as we like to label it in the UK) has its own top-level.
o "Modules" is now also on the top-level instead of being in the
"Calculate" menu.
Not everything made it:
o "Symmetry by Molecule" has been removed (for the moment).
o RCrane and the glycan builder have yet to be brought back to working
order.
o FLEV, QED breakouts and Chemical Feature Clusters are still missing.
I am grateful for the contributions from Jakub Smulski for help with
this over the last year and to Global Phasing for the funding. Martin
Noble has written the ribbon and surface representation code.
At the moment, the terminal output is a bit verbose with debugging output.
That will be reduced or removed in due course.
Although I've not tried it, I hope/expect that this Coot will run very
sweetly on a M2 Pro MacBook Pro... Having said that, "M2 good, M3 better" -
I suppose?
Source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.tar.gz
Binaries:
Binaries have always been issue with Coot. The problem is that a
project of the scale of Coot needs (at least) 3 people [2],
o one for the scientific developments/new algorithms and publications
o one for the development of the GUI (and graphics in the case of
Coot)
o one for the deployment of binaries - it takes time to produce
binaries
for numerous versions of numerous operating systems and the many
changing/improving dependencies (to me this feels like a constantly
changing, never complete jigsaw puzzle)
And, although I recognise its importance, I just keep dropping the ball
for the third one (is has little intrinsic pleasure for me and is
completely invisible career-wise).
Coot on "Linux":
There is a build-script, build-coot-3-3 that works for me, soup to
nuts on a modern Ubuntu system. Not so much on Fedora though. I will
try to help if you try this method and things go wrong. Python and
its add-ons are exquisitely tricky to build and is not well
documented,
however [3].
https://raw.githubusercontent.com/pemsley/coot/main/build-it-3-3
Coot on macOS:
Some Mac users might like to consider using Homebrew. At some stage
I hope that
$ brew install coot
will (just) work. But that will involve input from by Yoshitaka
Moriwaki who is looking after Coot in Homebrew (that might take a
month or two). Right now, Mac-using homebrew-using Coot
enthusiasts can follow issue 33 on github:
https://github.com/pemsley/coot/issues/33
Coot on "Windows":
Bernhard Lohkamp is the font of all wisdom when it comes to
WinCoot. He will let us know his schedule. (Within a month though,
that is my understanding.)
via CCP4:
In the coming weeks CCP4 will review Coot 1.1 and decide if it is
acceptable to be added to the suite. If approved, that is the path
of least effort for me and many users.
What about 0.9.x?
I will maintain the back-end/libraries until April 2024, then I will
reassess. It's just too much trouble to change the GUI though.
Future:
With such a massive change set [4], there are bound to be bugs, so I
imagine
a flurry of patch releases in the forthcoming weeks.
With this bad boy [5] out the door and with Lucrezia Catapano coming
back on-line I can spend more time on Moorhen [6] and the Blender
interface - hooray!
If you've got this far and can get this Coot to run, I have added an
Easter
Egg for today (I'll tell you what it is: coot.halloween()).
[1] To give you an idea of the scope of this work (and the speed at
which the
interface for Coot was implemented) look how long it takes to rewrite a
GUI:
https://fosspost.org/gtk-4-0-released/
[2] According to a Basic COCOMO model I found, a project of this size is the
output that can be expected from a team of 300 working for 56
months (make
of that what you will)
[3] https://www.bassi.io/articles/2022/12/02/on-pygobject
[4] The patch to go from 0.9.8.92 to 1.1 is 850k lines
[5] meanings 3 and 4 in the wiktionary
[6] moorhen.org
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