Activity for PyMOL Molecular Graphics System
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Thomas Holder modified ticket #196
pdb output from gromacs .gro file
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fixed in rev 4182
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pymol/bugs/196, pmw/bugs/47
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duplicate of https://sourceforge.net/p/pymol/bugs/186/
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autoplist doesn't record the correct installed file list
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regression of https://sourceforge.net/p/pymol/code/4181/
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pdb output from gromacs .gro file
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Stephane Rety created ticket #196
pdb output from gromacs .gro file
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Carlos Familia posted a comment on ticket #184
I also observe this problem on virtualbox with debian as guest system. It does not depend if it is the pymol provided by deb system or compiled from source.
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some elements wrong from SDF and XYZ
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Thanks for testing. Note that fetch caches the downloaded file in fetch_path (current directory by default) https://pymolwiki.org/index.php/Fetch_Path Using load with an https:// URL is a good alternative test (no caching): load https://files.rcsb.org/download/1UBQ.pdb Also works for me on MacOS Sierra (10.12) with MacPorts.
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I've run the second command on the console and it worked (on the non patched pymol), however i couldn't test the first command as after the first command was run it always worked, even after restarting the console, restarting the computer and reinstalling pymol.
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MacOS High Sierra with Python 2.7.14 installed via MacPorts
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I've seen this error when ssl libraries were not installed correctly. I can't reproduce this on my current test systems (e.g. Arch Linux with Python 2.7.14). What operating system do you use? Any proxy or firewall in use? Without patching, does fetching work after pasting this into the PyMOL command line? import ssl ssl._https_verify_certificates(enable=False) Or by exporting PYTHONHTTPSVERIFY=0 from the environment befor launching PyMOL? PYTHONHTTPSVERIFY=0 pymol
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Alois Schloegl posted a comment on ticket #184
Under certain circumstancies, (usually connecting to a debian server through ssh with X-tunneling), I observe als this behavior, and reported this on debian/pymol bug tracker https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=783653 When trying to figure out the cause for this, it seems the crash occurs when 256 bits are used in GL_RENDERER GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.8, 256 bits) When 128 bits is reported, it seems to work fine. I tried several Debian servers (jessie, jessie-backports,...
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Pymol gives error on fetching from any https site when build with python 2.7.14
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pse_export_version support with Python 3
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when you click on the image, you're discarding it and PyMOL switches back to real-time rendering. That also was the same in previous versions.
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Jack Howarth posted a comment on ticket #194
Doesn't this imply that the ray-trace demo needs to be tweaked to provide a more uniform experience? Having a demo which displays a checker board background when run but a black one when clicked on, seems a bit random in behavior.
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pymol 1.9.0.0 produces checkerboard in ray-tracing demo in HD 2600 XT
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This is a feature, not a bug, and it's controlled with the opaque_background setting. We've changed the default value of this setting in PyMOL 1.9. Run this in PyMOL 1.8 (or any older version) and you'll get the same result: set opaque_background, off wizard demo, ray
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pymol 1.9.0.0 produces checkerboard in ray-tracing demo in HD 2600 XT
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(svn propdel svn:executable)
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1.9.0.0
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PyMOL 2.0 should fix this. Please give the new version a try: https://pymol.org/2/ These improvement are not yet available in the open source repository.
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Boris Law created ticket #193
Pymol viewer contents doesn't fit in viewing window
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oneletter, wire/licorice, copy_to
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Hi Max - Would you mind testing my modified patch (tk-aqua-v2.patch)? It reuses more existing code. Also, please add a note or comment to this issue that you put your patch in the public domain or under a BSD-like license. For the record, this works for me with: - homebrew - system Python - anaconda It does not work with: - macports (tk +quartz), threading issues - GLUT framework instead of X11 freeglut Thomas
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make build reproducible
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Patch that fixes support for the external GUI running under the OS X native windowing system (Aqua)
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Hi Max - This is fantastic! Great work! I will do some heavy testing and see how this plays with the other available environments on macOS (macports, fink, anaconda, system python, GLUT framework, ...). Thomas
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pymol fails to build on High Sierra
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Max Klein posted a comment on ticket #13
Here's the latest verson of the patch, with a fix for a bug that showed up durring testing on Linux.
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Patch that fixes support for the external GUI running under the OS X native windowing system (Aqua)
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1.8.7.0
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Jon Phillips created ticket #191
Pymol segfaults on pdb load if user is not in video group
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Álvaro Serrano Morrás created ticket #190
Black Inner surface
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make build reproducible
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patch applied in svn rev 4175
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[linux] Pymol and webpy file conflict
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fixed in svn rev 4175 web.pymolhttpd -> pymol.pymolhttpd
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patches/12, bugs/148
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Yuri posted a comment on ticket #189
Found this while creating the FreeBSD port.
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autoplist doesn't record the correct installed file list
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This is not a PyMOL bug. Have you installed the autodock plugin from https://github.com/ADplugin/ADplugin ? You should file an issue there. You can also ask for help on the pymol-users mailing list: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Kelly McGuire created ticket #188
PyMOL Autodock Plugin Error
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Bernhard M. Wiedemann created ticket #12
make build reproducible
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label sele op, iterate/alter improvements, ...
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Jonb Sayers created ticket #187
Pymol crashes in Sierra
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PSE compatibility between Python 2 and 3
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patches welcome
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Python 3.6 fixes
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'install --record' doesn't record all files that PyMOL installs
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1.8.6.1 fixes
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PyMOL Molecular Graphics System released /pymol/1.8/pymol-v1.8.6.0.tar.bz2
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1.8.6.0
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mmtf fixes, documentation, auto-completion
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mmtf updates
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1.8.5.1 (beta)
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mpng width/height, pick_shading/surface_color_s...
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Executable permissions for data files
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molfile plugins, fetch URLs, ...
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will be fixed in r4165
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pseudoatom multi-state problem
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minor clang warnings in r4146
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const correctness has been heavily refactored since about r4089
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Improve const-correctness
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Log file Bug in v.099
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workaround: https://pymolwiki.org/index.php/Retain_order
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Selection argument "within" picks false residues
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fails to build on SuSE 10.0 x86_64
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selectionof residus in mol2 file
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fixed in PyMOL 1.8.2 (supports resn with unlimited number of characters)
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split_states * doesn't handle the wildcard correctly
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fixed in PyMOL 1.8.0
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fixed in Incentive PyMOL 1.8.4
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3Dconnexion 3D mouse support issue on Mac
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all the affected modules are not used anymore and have been removed from the contrib...
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different memory API for a given memory block
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1.8.5.0 (unstable/experimental)
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Exporting files
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PyMOL 1.8.4 adds map export in CCP4 format
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Incentive PyMOL 1.7.6 added chromadepth support for real-time rendering: https:/...
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apbstool plugin in pymol r4146 has python3 compatibility issues with pmw 2.0.0
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as I understand, all requested changes are not in PyMOL, but in third party depe...
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setup.py should compile .cpp files with g++ rather than gcc
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Since r4133, "monkeypatch_distutils.py" takes care of this. https://sourceforge....
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since r4133 we by default compile with -std=c++0x which also elimninates these w...
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many c++11-extensions warnings with current clang compilers
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pymol performs badly on Gallium 0.4 drivers from Fedora 25
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ProzacR created ticket #184
Segmentation fault in Linux virtualbox
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Andre created ticket #183
stereoscopic 3D quad buffered not working
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backport C++11 features for gcc-4.5
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Alexey Strokach modified a comment on ticket #173
I think this could be fixed by replacing all lines similar to '#%04x%04x%04x' % (lightRGB[0],...
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I think this could be fixed by replacing all lines similar to '#%04x%04x%04x' % (lightRGB[0],...
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I think this could be fixed by replacing '#%04x%04x%04x' % (lightRGB[0], lightRGB[1],...
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1.8.4.0
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Thomas Linsky posted a comment on ticket #182
That fixes the issue! Thank you!