Thank you for the hard work :) For many years now, Coot has been a mainstay of structural work and it is exciting to see the new release.
Artem On Tue, Oct 31, 2023, 1:10 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > 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 > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
