Re: [COOT] Release 0.8 Re: Coot performance on Intel HD
On 01/10/14 13:40, Marcin Wojdyr wrote: A few days ago I've reported the issue with squares to freeglut developers and they removed the points: https://github.com/dcnieho/FreeGLUT/issues/19 For the coming ccp4 release we'll go with stroke-characters enabled by default (for Linux only) and with patched freeglut. FWIW, I have made a patch to the coot source code in 0.8.1-pre for stroke character points. Paul.
Re: [COOT] Release 0.8
Dear Paul, currently, I have Coot installed via the CCP4 6.4 suite. Will the new version also be released over the CCP4 update manager? Best regards, Dirk. Am 23.09.2014 um 15:09 schrieb Paul Emsley: We are pleased to announce the release of Coot 0.8. New binaries should be on their way shortly: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/ http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/ o FEATURE: Added an interface for Cootilus o FEATURE: Pubchem support for drag and drop o FEATURE: Added glyo and ProSMART modules o FEATURE: Auto-open MTZ files with x.F_phi.F x.F_phi.phi for any value of x. o FEATURE: When input map seems to be from EM, ignore modal density values for statistics calculation o FEATURE: labels and on-screen text can now be rendered with stroke characters instead of bitmaps (set-use-stroke-characters 1) set_use_stroke_characters(1) o FEATURE: Enable the running of python commands from the command line o FEATURE: Install appdata for GNOME Software Center [Richard Hughes] o FEATURE: New program compare-dictionaries added o FEATURE: New program make-shelx-restraints added o FEATURE: pdb validation data parser and gui attached to Fetch accession code. o FEATURE: Added match-residue-and-dictionary() function for atom name matching of similar monomers o FEATURE: Added function to move a reference chain to a symmetry-related position o FEATURE: Add parallel nucleotide plane restraints o CHANGE: Bond colours against a white background have been improved o CHANGE: Main gui icons are now pngs o CHANGE: Pyrogen bundled in enhanced-ligand version o CHANGE: Deuteriums are pink o CHANGE: Extra restraints added to Raster3D input o CHANGE: Geman-McClure M-estimator used for extra distance restraints o BUG-FIX: CA-mode now works for MSEs o BUG-FIX: Mo bonding improved o BUG-FIX: Unbonded CA now have stars in CA mode o BUG-FIX: Better output of ligand fitting solutions [Andre White] o BUG-FIX: Adjust hydrogens also on nomenclature correction o BUG-FIX: Multi-solution ligand fitting fixed o BUG-FIX: Wedge bonds can now be converted to single bonds in LBG o BUG-FIX: Mol2 file atoms names are now preserved [Markus Rudolf] o BUG-FIX: B-factor colouring now fixed [Oliver Smart] o BUG-FIX: HOLE implementation handles large radii better o BUG-FIX: Improved SHELX .ins parsing [Dale Tronrud] o BUG-FIX: mmCIF output atom name quoting fix o BUG-FIX: atom quad type check test fix [David Binderman] -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [COOT] Release 0.8
On 30 September 2014 12:33, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: Dear Paul, currently, I have Coot installed via the CCP4 6.4 suite. Will the new version also be released over the CCP4 update manager? It will be included in CCP4 6.5 which is to be released in October. Marcin
Re: [COOT] Release 0.8 Re: Coot performance on Intel HD
On Friday, 26 September, 2014 17:47:44 Hattne, Johan wrote: On Sep 26, 2014, at 13:29, Ethan A Merritt merr...@u.washington.edu wrote: On Tuesday, 23 September, 2014 14:09:08 Paul Emsley wrote: We are pleased to announce the release of Coot 0.8. New binaries should be on their way shortly: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/ http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/ o FEATURE: labels and on-screen text can now be rendered with stroke characters instead of bitmaps (set-use-stroke-characters 1) set_use_stroke_characters(1) Great news! This fixes the Coot slow on Intel HD4000 graphics problem. Now the only problem is that your binary packages use a libpng version that is not compatible with the *.png icons supplied by my system. So I get a screenful of warnings on startup and all the icons show up blank. It's not your fault that libpng can't seem to get its act together and provide back/forward compatibility, but the problem could be worked around by including compatible icons in the binary package rather than referring to system-supplied icons that are version-dependent. This could be due to the minor zlib-header breakage caused by libpng 1.2.6”. If so, running the icons through png-fix-IDAT-windowsize [http://www.libpng.org/pub/png/apps/pngcheck.html] might help. Sure. But Coot is pointing to the system icon directories. I know how to convert the png images, but unless there is some trick I haven't thought of Coot will still be pointing to the system ones rather than the ones I have converted. And I'm certainly not about to go around re-processing all the system icons on every machine that might run Coot. I usually rebuild Coot from source, and I'll do that for the released version 0.8 as soon as I get some time. That way there are no library incompatibilities. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [COOT] Release 0.8 Re: Coot performance on Intel HD
On Sep 26, 2014, at 13:29, Ethan A Merritt merr...@u.washington.edu wrote: On Tuesday, 23 September, 2014 14:09:08 Paul Emsley wrote: We are pleased to announce the release of Coot 0.8. New binaries should be on their way shortly: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/ http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/ o FEATURE: labels and on-screen text can now be rendered with stroke characters instead of bitmaps (set-use-stroke-characters 1) set_use_stroke_characters(1) Great news! This fixes the Coot slow on Intel HD4000 graphics problem. Now the only problem is that your binary packages use a libpng version that is not compatible with the *.png icons supplied by my system. So I get a screenful of warnings on startup and all the icons show up blank. It's not your fault that libpng can't seem to get its act together and provide back/forward compatibility, but the problem could be worked around by including compatible icons in the binary package rather than referring to system-supplied icons that are version-dependent. This could be due to the minor zlib-header breakage caused by libpng 1.2.6”. If so, running the icons through png-fix-IDAT-windowsize [http://www.libpng.org/pub/png/apps/pngcheck.html] might help. // Johan Research Specialist @ Gonen Lab Janelia Farm Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [COOT] Release 0.8 Re: Coot performance on Intel HD
These artifacts are GL_POINTS. I'm a bit puzzled by this: https://github.com/dcnieho/FreeGLUT/blob/git_master/freeglut/freeglut/src/fg_font.c#L281 why glutStrokeCharacter() does GL_POINTS in addition to lines? Maybe it's only in freeglut or only in the latest freeglut versions, I haven't checked. I've made a quick fix locally and the labels look good. I guess Paul will provide a proper fix/workaround soon. Marcin On 26 September 2014 19:02, Marcin Wojdyr woj...@gmail.com wrote: On 26 September 2014 18:48, Ethan A Merritt merr...@u.washington.edu wrote: Indeed. But do you also get such font effect when zooming in: http://i.imgur.com/tg350vo.png ? No I don't, or at least I didn't see anything like that when testing last night. I'll check again this evening. Does the effect go away when you rotate? No, only when I zoom out. Marcin
Re: [COOT] Release 0.8 Re: Coot performance on Intel HD
On Friday, 26 September 2014 08:18:49 PM Marcin Wojdyr wrote: These artifacts are GL_POINTS. I'm a bit puzzled by this: https://github.com/dcnieho/FreeGLUT/blob/git_master/freeglut/freeglut/src/fg_font.c#L281 why glutStrokeCharacter() does GL_POINTS in addition to lines? Maybe it's only in freeglut or only in the latest freeglut versions, I haven't checked. I've made a quick fix locally and the labels look good. I guess Paul will provide a proper fix/workaround soon. I see nothing like that here. (screenshot: http://skuld.bmsc.washington.edu/~merritt/coot_08.png ) My machine has stonelion [2931] ldd coot-real | grep glut libglut.so.3 = /lib64/libglut.so.3 (0x7fd7e657b000) stonelion [2932] rpm -qf /lib64/libglut.so.3 lib64freeglut3-2.8.1-2.mga4 Ethan -- mail: Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[COOT] Release 0.8
We are pleased to announce the release of Coot 0.8. New binaries should be on their way shortly: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/ http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/ o FEATURE: Added an interface for Cootilus o FEATURE: Pubchem support for drag and drop o FEATURE: Added glyo and ProSMART modules o FEATURE: Auto-open MTZ files with x.F_phi.F x.F_phi.phi for any value of x. o FEATURE: When input map seems to be from EM, ignore modal density values for statistics calculation o FEATURE: labels and on-screen text can now be rendered with stroke characters instead of bitmaps (set-use-stroke-characters 1) set_use_stroke_characters(1) o FEATURE: Enable the running of python commands from the command line o FEATURE: Install appdata for GNOME Software Center [Richard Hughes] o FEATURE: New program compare-dictionaries added o FEATURE: New program make-shelx-restraints added o FEATURE: pdb validation data parser and gui attached to Fetch accession code. o FEATURE: Added match-residue-and-dictionary() function for atom name matching of similar monomers o FEATURE: Added function to move a reference chain to a symmetry-related position o FEATURE: Add parallel nucleotide plane restraints o CHANGE: Bond colours against a white background have been improved o CHANGE: Main gui icons are now pngs o CHANGE: Pyrogen bundled in enhanced-ligand version o CHANGE: Deuteriums are pink o CHANGE: Extra restraints added to Raster3D input o CHANGE: Geman-McClure M-estimator used for extra distance restraints o BUG-FIX: CA-mode now works for MSEs o BUG-FIX: Mo bonding improved o BUG-FIX: Unbonded CA now have stars in CA mode o BUG-FIX: Better output of ligand fitting solutions [Andre White] o BUG-FIX: Adjust hydrogens also on nomenclature correction o BUG-FIX: Multi-solution ligand fitting fixed o BUG-FIX: Wedge bonds can now be converted to single bonds in LBG o BUG-FIX: Mol2 file atoms names are now preserved [Markus Rudolf] o BUG-FIX: B-factor colouring now fixed [Oliver Smart] o BUG-FIX: HOLE implementation handles large radii better o BUG-FIX: Improved SHELX .ins parsing [Dale Tronrud] o BUG-FIX: mmCIF output atom name quoting fix o BUG-FIX: atom quad type check test fix [David Binderman]
