Activity for PyMOL Molecular Graphics System
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Alberto Renee Mora Peña posted a comment on a wiki page
i need help please We have observed that when performing superpositions, the visual aid links between corresponding atoms are sometimes displayed in yellow and, in other cases, in purple. We have been trying to understand the underlying logic that determines this color difference. For instance, we've noticed that complex, non-local, or multi-part superpositions sometimes result in purple links, while simpler alignments often result in yellow ones, but this is not always consistent. Our working hypothesis...
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Pooja Sarngadharan posted a comment on a wiki page
Hi, I have troubles with h_add in Pymol. I was modelling some ligand molecules in PDB format and needed to add hydrogens (eg. chlorophyll A). When h_add is used, Pymol is randomly filling up all the valencies of carbon atoms by adding hydrogen without identifying the double and triple bonds. Is there a way to rectify this or is it a bug needs to be solved? Thanks in advance!
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Maryam posted a comment on a wiki page
Hi I have few qauestions related to interface residues script if you could please answer In interfaceResidue script,def interfaceResidues(cmpx, cA='c. A', cB='c. B', cutoff=1.0, selName="interface"): here dASA cutoff is 1.0. How to decide this cutoff value? My second question is Is it possible to get the values dASA of the complex and individual chains (calculated through the interfaceResidue.py script in PyMol) printed into any txt or excel sheet?
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Artik Bohm posted a comment on ticket #173
Probably a hack more than a patch, but I fixed it by casting to int(): '#%04x%04x%04x' % (int(lightRGB[0]), int(lightRGB[1]), int(lightRGB[2])), '#%04x%04x%04x' % (int(darkRGB[0]), int(darkRGB[1]), int(darkRGB[2]))
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vanessa natera posted a comment on a wiki page
Hi , I am using open source pymol to make a movie and I am having a difficult time finding a work around to use the morphing feauture. Is there anyone who knows a way to use morphing/something similar in open source pymol?
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Thomas Holder posted a comment on a wiki page
Hi Patricia - Can you ask this question on the pymol-users mailing list? You need to subscribe first at http://pymol.org/maillist and then you can send emails to the list.
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Patricia Rea posted a comment on a wiki page
Hi – I’m a high school student learning to use Pymol for my science fair research, and I’ve been using Pymol for about 6 months. I have been working on attempting to bind a protein to actin for over a month now – but whenever I fuse the linker to the antifreeze protein, it glitches. As well, when I save my actin chain with all the linkers fused as a PDB file and reopen it, only one of the linkers is visible. I’m hoping you might be able to help me figure out what I’m doing wrong. Schrodenger support...
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Home
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What does PyMOL 1.8 report as "OpenGL graphics engine" and what OpenGL version does it detect?
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santiago miranda posted a comment on ticket #210
Hi Thomas, Thank you. uhmm yes but I can't open any .pdb file the only workaround was to install an older version of PyMOL and open the files with an older version (1.8)
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Does it work headless? pymol -c scriptt.pml This looks suspicious: "OpenGL Renderer : (Unknown)"
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-Computer specs- Processor : AMD A12-9720P RADEON R7, 12 COMPUTE CORES 4C+8G Memory : 7603MB (3084MB used) Machine Type : Notebook Operating System : Ubuntu 18.04.2 LTS Date/Time : Fri 05 Apr 2019 19:41:04 BST -Display- Resolution : 1366x768 pixels OpenGL Renderer : (Unknown) X11 Vendor : The X.Org Foundation -Audio Devices- Audio Adapter : HDA-Intel - HDA ATI HDMI Audio Adapter : HDA-Intel - HD-Audio Generic EPSON_WF_2750_Series@EPSON85C2A6.local HP_Deskjet_3050A_J611_series_2_Evelyn_s_MacBook_Air...
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executing pymol script from shell
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enable vmd plugins by default
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cartoon_transparency doesn't support residue/chain based sel
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Implemented in PyMOL 2.3
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[linux] PyMOL windows not associated with pid
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works in PyMOL 2.0
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Home
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Issue with wildcard use preceding "_" in object selection
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fixed in svn rev 4190 - will be fixed in Incentive PyMOL 2.2
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fix wildcard, fix PDB 99999 crash, PQR parsing...
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Issue with wildcard use preceding "_" in object selection
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Vladas Oleinikovas posted a comment on ticket #209
P.S. My version here is 1.7.4, but I have the same issue with 2.0.7.
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Issue with wildcard use preceding "_" in object selection
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NaskoMak created ticket #208
pymol 2.1.0 on Mac OS 10.13.4 with python3 and pyqt5 can't find opengl engine
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Jennifer Channell created ticket #207
ray in maximum quality causes damfilt model to disappear
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Does the same error occur if you type this into the PyMOL command line? fetch 3CX5 If yes, can you please type "diagnostics" into the PyMOL command line, then copy the output and paste it here as a comment? This will contain information about your graphics driver etc. diagnostics
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modules not built with -O3 like main pymol files
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-fno-strict-aliasing patch applied in svn rev 4189
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anaglyph batch mode, all_states measurements, ...
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le created ticket #206
error to load a specif pdp format file
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Jack Howarth posted a comment on ticket #205
FYI, the issue appears to be either fixed or latent in current clang/llvm trunk for the 7.0 release. However Apple is conservative about absorbing changes from llvm.org so we need to file a radar to make sure they test that this issue if fixed in the next major Xcode release.
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is this issue resolved for you? It works fine in my hands, doing "/opt/local/bin/python setup.py --no-user-cfg install --prefix=... --root=..." installs everything.
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FYI, the preprocessed failing test case doesn't trigger on ubuntu bionic using the same clang 6.0.0 release so the issue appears to be entirely darwin specific. The proposed fix of restricting the addition of -fno-strict-aliasing to darwin should be appropriate.
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modules not built with -O3 like main pymol files
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Thanks Jack for figuring this out! Your patch looks good.
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Note that I opened https://bugs.llvm.org/show_bug.cgi?id=37280 with the upstream llvm clang developers.
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I would also note that, on darwin, we seem to automatically get -fno-strict-aliasing appended to compilations of c code through setup.py but not c++ code. Hence the need to explicitly pass -fno-strict-aliasing in setup.py on darwin. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1...
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I would also note that, on darwin, we seem to automatically get -fno-strict-aliasing appended to compilations of c code through setup.py but not c++ code. Hence the need to explicitly pass -fno-strict-aliasing in setup.py on darwin. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -pipe -Os -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1...
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This issue can be fixed far more gracefully with the following change to setup.py... Index: setup.py =================================================================== --- setup.py (revision 4187) +++ setup.py (working copy) @@ -392,12 +392,12 @@ libs += ["GLEW"] libs += pyogl_libs - ext_comp_args += ["-ffast-math", "-funroll-loops", "-fcommon"] + ext_comp_args += ["-ffast-math", "-funroll-loops", "-fcommon", "-O3"] # optimization currently causes a clang segfault on OS X 10.9 when # compiling layer2/RepCylBond.cpp...
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Opps. I missed that you are disabling -O3 on darwin. It would be better to enhance that with a check the offending compiler version of clang instead of all versions of clang.
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modules not built with -O3 like main pymol files
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The problem is in the fink and macports packaging which was based on a much earlier behavior of PYMOL_PATH. Setting it to PYMOL_PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/pymol_path instead of PYMOL_PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol eliminated the need for the redundant installation of the subdirectories associated with pymol_path.
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Does the incentive build install the modules subdirectory? I don't recall it having APBS Tools plugin. Perhaps it has been omitted by accident because of that.
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This is using the MacPorts python packaging for the 2.7 and 3.x series using the Python port group for installing python packages. https://guide.macports.org/chunked/reference.portgroup.html which should be installing pymol with.... ${python.bin} setup.py install --no-user-cfg --prefix=${python.prefix} --root=${destroot} Note that the fink packaging system sees the same issue... https://github.com/fink/fink-distributions/blob/master/10.9-libcxx/stable/main/finkinfo/sci/pymol-py.info and the modules...
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This is using the MacPorts python packaging for the 2.7 and 3.x series using the Python port group for installing python packages. https://guide.macports.org/chunked/reference.portgroup.html which should be installing pymol with.... ${python.bin} setup.py --no-user-cfg --prefix=${python.prefix} --root=${destroot}
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what do you mean by it's not installed? What's your manual step?
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The actual problem stems from setup.py not installing the modules directory. Is there a reason why we have to manually install that directory?
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FYI, the current 2.1.0 release with PyQt support can be built under MacPorts with the proposed packaging changes at https://trac.macports.org/ticket/56139 .
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FYI, the current 2.1.0 release with PyQt support can be built under MacPorts with the proposed packaging changes at https://trac.macports.org/ticket/56139.
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pymol install doesn't compile python scripts in modules
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Please use /bin/sh instead of /bin/bash in bin/pymol
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fixed in rev 4188
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2.2.0a0 (unstable/experimental)
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Showing surface with the legacy APBS plugin and PyQt PyMOL interface works for me on Linux. They way how pdb2pqr is imported is messy, that could ceratinly be improved.
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I have managed to get the APBS plugin to work partially under a MacPorts build of pymol with the PyQT interface as long the tk and pmg components are installed. However,, while I can use the APBS plugin to generate electrostatic maps for a pdb file, when I try to display the electrostatic surface, pymol goes into an endless cycle of progress bars being displayed. Have you been able to get the APBS plugin to render surfaces when pymol is run under the PyQt interface?
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I have managed to get the APBS plugin to work partially under a MacPorts build of pymol with the PyQT interface as long the tk and pmg components are installed. However,, while I can use the APBS plugin to generate electrostatic maps for a pdb file, when I try to display the electrostatic surface, pymol goes into an endless cycle . of progress bars being displayed. Have you been able to get the APBS plugin to render surfaces when pymol is run under the PyQt interface?
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these plugins can be disabled in the Plugin Manager (Plugin > Plugin Manager > ... > [ ] Load on startup). After that no Tkinter errors should be raised.
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It's possible to select the tk interface over pyqt at run time like this: pymol -N pmg_tk
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Just to clarify the situation with building pymol with PyQt support on MacPorts vs fink, currently only MacPorts will be able to produce a working pymol using the PyQt support. The issue appears to be that fink's glew package is built against the X11 libGL (which is a wrappered version providing additional X11 support to libGL) whereas the MacPorts glew package is built against the system libGL instead. Also, it is necessary to build pymol with the --osx-framworks option passed to setup.py to avoid...
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Note that the MacPorts test packaging for pymol 2.1.0 at https://trac.macports.org/ticket/56139 reveals that when built for X11 tk support, the resulting pymol, when started in the presence of PyQt, will fail to properly initialize its GL support.... Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 0.0. OpenGL graphics engine: GL_VENDOR: (null) GL_RENDERER: (null) GL_VERSION: (null) Detected 8 CPU cores. Enabled multithreaded rendering. Deinstalling the PyQt package...
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Note that I have posted initial packaging changes to the MacPorts pymol package for builds with either the X11 or PyQt support. https://trac.macports.org/ticket/56139
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run time option to disable use of PyQt should be added
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QT support not fully decoupled from Tk support
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what kind of graphics card and driver? (though I'm not familiar with the driver situation on BSD) which Qt version? (e.g. 5.6) "blinking" indicates that the context doesn't have double buffering. Try forcing mono (skipping quad buffer request) by launching with "-M": pymol -M
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what kind of graphics card and driver? (though I'm not familiar with the driver situation on BSD) which Qt version? (e.g. 5.6) "blicking" indicates that the context doesn't have double buffering. Try forcing mono (skipping quad buffer request) by launching with "-M": pymol -M
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Yuri posted a comment on ticket #201
OpenGL area also blinks.
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I'm also getting this: WARNING: glDrawBuffer caused GL error All with PyQt5 UI.
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Allow plugin installation into user's home directory
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This is already possible: Plugin Manager > Settings > Add new directory ...
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WARNING: glReadBuffer caused GL error 0x0502
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Allow plugin installation into user's home directory
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Please use /bin/sh instead of /bin/bash in bin/pymol
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Please use /bin/sh instead of /bin/bash in bin/pymol
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PyMOL Molecular Graphics System released /pymol/2/pymol-v2.1.0.tar.bz2
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Pymol viewer contents doesn't fit in viewing window
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Pymol viewer contents doesn't fit in viewing window
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should be fixed in svn rev 4187
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warning: 'gluPerspective' is deprecated: first deprecated in OS X 10.9 - "Use GLKMatrix4MakePerspective"
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GLU dependency removed in svn rev 4187
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PyQt interface (2.1.0)
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Ticket moved from /p/pymol/bugs/198/
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Please post questions like that to the pymol-users mailing list: https://sourceforge.net/projects/pymol/lists/pymol-users Also, if you provide a specific example (e.g. PDB codes) it will be much more likely that someone understands the problem and can help you. "super" aligns on structure only (sequence independent) as well. See: https://pymolwiki.org/index.php/Align https://pymolwiki.org/index.php/Super https://pymolwiki.org/index.php/Cealign
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Grace Ferri created ticket #198
Does a poor alignment in cealign negate a good alignment in super?
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stick_round_nub, UTF-8, display_scale_factor, ...
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For the record: diff --git a/layer1/Scene.cpp b/layer1/Scene.cpp index 90ef6d6d6..d8d66f3b4 100644 --- a/layer1/Scene.cpp +++ b/layer1/Scene.cpp @@ -9144,8 +9144,9 @@ void SceneRender(PyMOLGlobals * G, Picking * pick, int x, int y, curState = SettingGetGlobal_i(G, cSetting_state) - 1; } if(!SettingGetGlobal_b(G, cSetting_ortho)) { - float fov = SettingGetGlobal_f(G, cSetting_field_of_view); - gluPerspective(fov, aspRat, I->FrontSafe, I->BackSafe); + height = I->FrontSafe * GetFovWidth(G) / 2.f; +...
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polymer.protein polymer.nucleic multifilesave ...
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Christoph Gohlke posted a comment on ticket #197
Works for me. Thank you.
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I haven't gotten any feedback on my revised patch (tk-aqua-v2.patch). Is there still interest is getting this patch in?
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Heads-up: async is a keyword in Python 3.7
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fixed in rev 4184. Renamed all async variables to async_ (trailing underscore). Backwards compatibility of function keyword arguments is handled with **kwargs.
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py37, align alt, flag 6+7
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Heads-up: async is a keyword in Python 3.7
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Thanks Christoph!
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Heads-up: async is a keyword in Python 3.7
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auto library mode