[COOT] coot-1 on mac m1
Hi Paul, This release looks really interesting! Do you have any tips on compiling it for arm64 based archs (m1 and ilk)? There appears to be a dependency on fftw2 which I am failing to compile on the M1. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK 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/
Re: [COOT] Coot 1
Hi Paul, The new Coot does have a nice depth of field and that certainly helps to provide a 3D feeling to the image. Still, I hope you can manage to bring it back at some future date. Old habits die hard... Best, Pedro Em 01/04/2022 12:03, Paul Emsley escreveu: Hi Pedro, Stereo is not available because I didn't have access to stereo at home and I have not been keen on touching communal equipment at the lab. My guess is that it needs only 100 lines or so - many of those are in Coot 0.9.x. I would like a chance to revisit the view matrices though - during a recent test of new stereo kit PyMOL was noticeably better. I wonder actually if stereo is so necessary in Coot 1 though..? - here's a side-by-side. Paul On 01/04/2022 11:32, Pedro Matias wrote: Hi Paul, Is stereo definitely off the table for Coot 1 or will you add it back later? If not, the I would ask CCP4 developers to *pretty please* keep coot 0.9 as a legacy option for us users who cannot live without stereo. 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/ -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 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/
Re: [COOT] Coot 1
Hi Paul, Is stereo definitely off the table for Coot 1 or will you add it back later? If not, the I would ask CCP4 developers to *pretty please* keep coot 0.9 as a legacy option for us users who cannot live without stereo. Best, Pedro Em 01/04/2022 11:14, Paul Emsley escreveu: 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 COOT list, click the
[COOT] 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 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/
