Re: [ccp4bb] Coot 1
Isn’t that what we all say every year on the day after March finishes? Harry > On 1 Apr 2022, at 23:46, Paul Emsley wrote: > > That, for the record, is more or less what Ralf said 18 years ago. > On 01/04/2022 23:38, Pavel Afonine wrote: >> It's April 1st today, isn't it? -;) >> >> >> On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley wrote: >> Coot 1 >> >> 18 years after the release of Coot 0 it's time that I actually released >> Coot 1. >> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] RES: [ccp4bb] Coot 1
If Paul had said that there is also a Windows version I would be sure that it was April fools’ joke. I can’t wait to use it Best Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acompanha uma mente bem treinada" De: Jurgen Bosch<mailto:jxb...@case.edu> Enviado:sexta-feira, 1 de abril de 2022 19:59 Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Assunto: Re: [ccp4bb] Coot 1 Yay!! I can now blend it with blender. Jürgen __ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology On Apr 1, 2022, at 18:46, Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: That, for the record, is more or less what Ralf said 18 years ago. On 01/04/2022 23:38, Pavel Afonine wrote: It's April 1st today, isn't it? -;) On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: Coot 1 18 years after the release of Coot 0 it's time that I actually released Coot 1. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Coot 1
Yay!! I can now blend it with blender. Jürgen __ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology On Apr 1, 2022, at 18:46, Paul Emsley wrote: That, for the record, is more or less what Ralf said 18 years ago. On 01/04/2022 23:38, Pavel Afonine wrote: It's April 1st today, isn't it? -;) On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley wrote: > Coot 1 > > 18 years after the release of Coot 0 it's time that I actually released > Coot 1. > > -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Coot 1
That, for the record, is more or less what Ralf said 18 years ago. On 01/04/2022 23:38, Pavel Afonine wrote: It's April 1st today, isn't it? -;) On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley wrote: Coot 1 18 years after the release of Coot 0 it's time that I actually released Coot 1. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Coot 1
It's April 1st today, isn't it? -;) On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley wrote: > Coot 1 > > 18 years after the release of Coot 0 it's time that I actually released > Coot 1. > > Coot 1 is a major change beyond Coot 0. It has required a lot of writing > and rewriting [1] > and has been the preponderance of my work since 2017. I have had to > learn how to program > graphics from scratch using the new style. Much of the GUI internals has > been > rewritten [2]. > > My experience with 0.9 was that I sat on it, bug-fixing for a long time, > releasing it > too late. I don't want to repeat that mistake. So here we are, there's a > lot of good new > stuff in Coot 1, but it's not as slick as it might be (or will become). > >o Update graphics to use OpenGL 3.3 >o Update Python to use version 3.9 >o Update GTK+ to use version 3 > > While many of the features that were available in 0.9.x have been > reworked or > re-implemented, there are some gaps. Dropped features include > Cross-hairs, Stereo, Pisa > interface, built-in key-bindings, NCS Ghosts, Edit Phi/Psi, > anti-aliasing, Kleywegt > plots, the clipping dialog, Chemical Feature Clustering, > Dynamically-Transformed/NCS > Maps, LSQ plane distances, dynamic distances, CABLAM-markup, the test > suite, > user-defined colour schemes, anisotropic atoms, CURLEW, Scheme GUI > scripting, > Skeletonization and Baton-Building. > > "So, is there anything that _does_ work?" - you might ask... > > The GUI has been updated, I have tried to cut down on the number of > dialogs, the Real > Space Refinement in particular has seen quite a lot of work. The GUI now > uses dark mode > if the theme is installed [3]. Several menu items have been relocated. > More menus are now > alphabetically ordered [4]. > > The graphics is, by default, now based on triangles instead of lines > which affords a > more pleasing representation (density maps can be represented using both > modes) and one > can have a more expeditious if not pleasant experience with a fast > graphics card and a > big screen. The various graphics effects and filters can be tailored to > some extent by > changing the configuration using the GUI or by editing/replacing the > shaders. > Full-screen mode is now an option [5]. > > Overall, the GUI has only had light testing. At the moment, it's > probably best to > avoid closing dialogs using the window manager. The "OK" button now > appears after the > "Cancel" button in dialogs. > > Python scripting now has uses a history from previous sessions and the > functions need > to be used with namespaces/modules (e.g. "coot", or "coot_utils"). Coot > (or coot) is > now a module that can be imported into python. > > This build compiles with the RDKit and optionally MoleculestoTriangles > from Martin Noble. > > The map and the model can now be exported to glTF files (for use in > Blender and other > 3D modelling software). > > The build script for Coot 1, called build-it-3-3 can be found in the > "Build from Scratch" > menu on the web page (you will need to have already installed cmake and > Gtk+). The catch > though is that (at least in my hands) Python and friends are > frustratingly difficult to > install, so it's possible/likely that the build script won't work. > Likewise, > the script doesn't work for Mac OS either. But it is currently the best > method to get > binaries so I will support it if you try it [6]. (Homebrew might be > another method.) > > Bernhard Lohkamp has been working on the WinCoot version - I will defer > WinCoot > questions to him. > > Mac Coot is now native (no X11/XQuartz needed). I would be interested to > see how a > natively-compiled [7] version works on an M1 Max processor [8,9]. > > Judging from previous experience, a few rapid iterations of bug-fix > releases will be > needed. After this, the version numbers will become sane - it's my plan > to release a new > major version every year or so. > > > https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.tar.gz > > Normally I don't cross-post releases, but this one I thought I should. > > > [1] new as in OpenGL 3.3 or later - using shaders - I don't mean Vulkan > (that's for the > future) > [2] the patch from the 0.9.x version is 285k lines > [3] I recommend it > [4] rather than chronologically > [5] double-tap Esc key (the first time) to revert to standard display > [6] I have be working with CCP4 collaborators to use their system to > build Coot binaries. > Hopefully the binaries will be available stand-alone, as well as > integrated into > the CCP4 Suite via that method > [7] so that's a different meaning of "native" > [8] the little testing I have done on a recent intel MacBook Pro shows > unimpressive > performance (Iris graphics, retina display) > [9] Thanks to my Mac-using colleagues for their feedback. > > > > To unsubscribe from the CCP4BB list, click the
[ccp4bb] Coot 1
Coot 1 18 years after the release of Coot 0 it's time that I actually released Coot 1. Coot 1 is a major change beyond Coot 0. It has required a lot of writing and rewriting [1] and has been the preponderance of my work since 2017. I have had to learn how to program graphics from scratch using the new style. Much of the GUI internals has been rewritten [2]. My experience with 0.9 was that I sat on it, bug-fixing for a long time, releasing it too late. I don't want to repeat that mistake. So here we are, there's a lot of good new stuff in Coot 1, but it's not as slick as it might be (or will become). o Update graphics to use OpenGL 3.3 o Update Python to use version 3.9 o Update GTK+ to use version 3 While many of the features that were available in 0.9.x have been reworked or re-implemented, there are some gaps. Dropped features include Cross-hairs, Stereo, Pisa interface, built-in key-bindings, NCS Ghosts, Edit Phi/Psi, anti-aliasing, Kleywegt plots, the clipping dialog, Chemical Feature Clustering, Dynamically-Transformed/NCS Maps, LSQ plane distances, dynamic distances, CABLAM-markup, the test suite, user-defined colour schemes, anisotropic atoms, CURLEW, Scheme GUI scripting, Skeletonization and Baton-Building. "So, is there anything that _does_ work?" - you might ask... The GUI has been updated, I have tried to cut down on the number of dialogs, the Real Space Refinement in particular has seen quite a lot of work. The GUI now uses dark mode if the theme is installed [3]. Several menu items have been relocated. More menus are now alphabetically ordered [4]. The graphics is, by default, now based on triangles instead of lines which affords a more pleasing representation (density maps can be represented using both modes) and one can have a more expeditious if not pleasant experience with a fast graphics card and a big screen. The various graphics effects and filters can be tailored to some extent by changing the configuration using the GUI or by editing/replacing the shaders. Full-screen mode is now an option [5]. Overall, the GUI has only had light testing. At the moment, it's probably best to avoid closing dialogs using the window manager. The "OK" button now appears after the "Cancel" button in dialogs. Python scripting now has uses a history from previous sessions and the functions need to be used with namespaces/modules (e.g. "coot", or "coot_utils"). Coot (or coot) is now a module that can be imported into python. This build compiles with the RDKit and optionally MoleculestoTriangles from Martin Noble. The map and the model can now be exported to glTF files (for use in Blender and other 3D modelling software). The build script for Coot 1, called build-it-3-3 can be found in the "Build from Scratch" menu on the web page (you will need to have already installed cmake and Gtk+). The catch though is that (at least in my hands) Python and friends are frustratingly difficult to install, so it's possible/likely that the build script won't work. Likewise, the script doesn't work for Mac OS either. But it is currently the best method to get binaries so I will support it if you try it [6]. (Homebrew might be another method.) Bernhard Lohkamp has been working on the WinCoot version - I will defer WinCoot questions to him. Mac Coot is now native (no X11/XQuartz needed). I would be interested to see how a natively-compiled [7] version works on an M1 Max processor [8,9]. Judging from previous experience, a few rapid iterations of bug-fix releases will be needed. After this, the version numbers will become sane - it's my plan to release a new major version every year or so. https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.tar.gz Normally I don't cross-post releases, but this one I thought I should. [1] new as in OpenGL 3.3 or later - using shaders - I don't mean Vulkan (that's for the future) [2] the patch from the 0.9.x version is 285k lines [3] I recommend it [4] rather than chronologically [5] double-tap Esc key (the first time) to revert to standard display [6] I have be working with CCP4 collaborators to use their system to build Coot binaries. Hopefully the binaries will be available stand-alone, as well as integrated into the CCP4 Suite via that method [7] so that's a different meaning of "native" [8] the little testing I have done on a recent intel MacBook Pro shows unimpressive performance (Iris graphics, retina display) [9] Thanks to my Mac-using colleagues for their feedback. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
