Re: [PyMOL] pymol installation error
Dear Mr. Jarrett, Yes, with the glm of version 0.0.9, pymol can be installed successful. Thank you very much:) -- From:Jarrett Johnson Send Time:2021年9月13日(星期一) 01:30 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] pymol installation error Hello, Looks like the glm version that you're currently using (I'm assuming 0.9.6--default package for Centos 7) is not up to date with the ones we're currently using (0.9.9). The location for glm headers within their library have changed a bit since the last several years. I might have to think of a way to reconcile these issues sometime this week. In the meantime if you'd like, I suggest picking up the latest package from https://github.com/g-truc/glm; alternatively, currently stick with your version and include and use `glm::epsilonEqual` over `glm::equal` on lines 31 and 32 of that source file. Hope that helps, Jarrett J On Sun, Sep 12, 2021 at 4:41 AM sunyeping via PyMOL-users wrote: Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’
Re: [PyMOL] pymol installation error
Hello, Looks like the glm version that you're currently using (I'm assuming 0.9.6--default package for Centos 7) is not up to date with the ones we're currently using (0.9.9). The location for glm headers within their library have changed a bit since the last several years. I might have to think of a way to reconcile these issues sometime this week. In the meantime if you'd like, I suggest picking up the latest package from https://github.com/g-truc/glm; alternatively, currently stick with your version and include and use `glm::epsilonEqual` over `glm::equal` on lines 31 and 32 of that source file. Hope that helps, Jarrett J On Sun, Sep 12, 2021 at 4:41 AM sunyeping via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > Dear all, > > Now I revised Line 4 in the SceneView.cpp file from > "#include " to > "#include ". > The error "layer1/SceneView.cpp:4:41: fatal error: > glm/ext/vector_relational.hpp: No such file or directory" > disappeared, but a now error appeared: > > layer1/SceneView.cpp:31:55: error: no matching function for call to > ‘equal(const vec3&, const vec3&, float)’ > Do you know how to deal with such an eorror? > > With many thanks! > Best regards > > -- > From:pymol-users > Send Time:2021年9月12日(星期日) 15:39 > To:pymol-users > Subject:[PyMOL] pymol installation error > > Dear pymol users, > > I am installing pymol in Centos 7 according to the guide in > https://pymolwiki.org/index.php/Linux_Install. I encounter an error of > "error: command 'g++' failed with exit status 1". A fill output of the > install command is as following: > > running build > running build_py > running build_ext > building 'pymol._cmd' extension > > g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat > -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE > -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC > -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include > -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 > -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src > -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include > -I/home/sunyp/software/anaconda/build/include > -I/home/sunyp/software/anaconda/build/include/freetype2 > -I/home/sunyp/software/anaconda/build/include/libxml2 > -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD > layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o > -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing > -Wno-char-subscripts -O3 -fopenmp > > g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat > -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE > -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC > -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include > -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 > -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src > -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include > -I/home/sunyp/software/anaconda/build/include > -I/home/sunyp/software/anaconda/build/include/freetype2 > -I/home/sunyp/software/anaconda/build/include/libxml2 > -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD > layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o > -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing > -Wno-char-subscripts -O3 -fopenmp > > g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat > -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE > -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC > -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include > -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 > -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src > -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include > -I/home/sunyp/software/anaconda/build/include > -I/home/sunyp/software/anaconda/build/include/freetype2 > -I/home/sunyp/software/anaconda/build/include/libxml2 > -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD > layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o > -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing > -Wno-char-subscripts -O3 -fopenmp > layer1/SceneView.cpp:4:41: > fatal error: glm/ext/vector_relational.hpp: No such file or directory > #include > ^ > compilation terminated. > > layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const > float*, int)’: > layer1/Scene.cpp:2557:42: > error: no matching function for call to ‘make_vec3(glm::vec3&)’ > > I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ > ^ >
Re: [PyMOL] pymol installation error
Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate
Re: [PyMOL] PyMOL installation on Windows 7
Looks like pip is not installed correctly or your PYTHONPATH wrong (unset it). To install pymol from wheels for Python 2.7 64 bit installed at C:\Python27, download the following files: pip-6.0.8-py2.py3-none-any.whl numpy-1.9.2+mkl-cp27-none-win_amd64.whl Pmw-2.0.0-py2-none-any.whl pymol-1.7.2.1-cp27-none-win_amd64.whl pymol_launcher-1.0-cp27-none-win_amd64.whl Then run this command from the folder containing the downloaded.whl files: C:\Python27\python.exe pip-6.0.8-py2.py3-none-any.whl/pip install --no-index --find-links=%CD% pymol_launcher Christoph On 3/13/2015 4:17 AM, Brenton Horne wrote: Oh, I have something else. Running in command prompt in admin mode I receive this error when running these whl installation commands: Traceback (most recent call last): File C:\Python27\lib\runpy.py, line 162, in _run_module_as_main __main__, fname, loader, pkg_name) File C:\Python27\lib\runpy.py, line 72, in _run_code exec code in run_globals File C:\Python27\Scripts\pip2.exe\__main__.py, line 5, in module ImportError: No module named pip On 13/03/2015 9:04 PM, Brenton Horne wrote: Hi, I have tried installing PyMOL via pip wheel files (found here http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol) using python 2.7.9 and while no obvious errors occurred during the execution of the |pip install ...| commands I have no new files in |C:\Python27|, my python directory. I have allowed for the fact that pip for me is at |C:\Python27\Scripts\pip2.exe| instead of |C:\Python27\Scripts\pip.exe| like I understand it usually is, as far as adjusting the PYTHONPATH variable accordingly. Any ideas on how to install PyMOL on my 64 bit Windows 7 SP1 OS? I have VisualStudio 2010 installed on my PC if relevant. If you need any other details please ask! Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now.http://goparallel.sourceforge.net/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL installation on Windows 7
Oh, I have something else. Running in command prompt in admin mode I receive this error when running these whl installation commands: Traceback (most recent call last): File C:\Python27\lib\runpy.py, line 162, in _run_module_as_main __main__, fname, loader, pkg_name) File C:\Python27\lib\runpy.py, line 72, in _run_code exec code in run_globals File C:\Python27\Scripts\pip2.exe\__main__.py, line 5, in module ImportError: No module named pip On 13/03/2015 9:04 PM, Brenton Horne wrote: Hi, I have tried installing PyMOL via pip wheel files (found here http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol) using python 2.7.9 and while no obvious errors occurred during the execution of the |pip install ...| commands I have no new files in |C:\Python27|, my python directory. I have allowed for the fact that pip for me is at |C:\Python27\Scripts\pip2.exe| instead of |C:\Python27\Scripts\pip.exe| like I understand it usually is, as far as adjusting the PYTHONPATH variable accordingly. Any ideas on how to install PyMOL on my 64 bit Windows 7 SP1 OS? I have VisualStudio 2010 installed on my PC if relevant. If you need any other details please ask! Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL installation
Both fink and macports have pymol packages. -David On Jun 15, 2011, at 10:37 AM, Spyros Charonis s.charo...@gmail.com wrote: Dear PyMOL community, I'm trying to get started with PyMOL, and the compilation is going wrong. After running python steup.py install on the terminal (I'm using OS X Snow Leopard) it complains with: GLEW_OK’ undeclared (first use in this function) lipo: can't open input file: /var/folders/Bh/Bh0rlnl0EkaDSfgci7c2Tk+++TQ/-Tmp-//ccp9fTEl.out I downloaded GLEW library but the compilation is still unsuccessful. Is there another way to get PyMOL running? Thanks in advance! Spyros -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol installation probs on ubuntu
Christoph, The message Could not find platform independent libraries prefix Consider setting $PYTHONHOME to prefix[:exec_prefix] indicates that Python is not being initialized properly. You may need to set PYTHONHOME explicitly in the pymol startup script. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for participating! -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Christoph Kaiser Sent: Friday, December 29, 2006 11:22 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol installation probs on ubuntu Hello, sorry for mybe asking stupid beginner's questions, but that's actually what i am ;-) i just tried to get pymol running on ubuntu. turns aout to ba a problem. i have python 2.4, 2.3 and 2.2 installed via the synaptic package manager, but when i tried to add pymol - also by synaptic - i already got some probs, as it was not able to find some moduels. i could fix this problem by changing the environment variables in the python start script. now i ran into the following prob, for which i can't find any solution: christ...@richterpc1:/usr/lib/python2.4/site-packages/pymol$ pymol Could not find platform independent libraries prefix Consider setting $PYTHONHOME to prefix[:exec_prefix] Traceback (most recent call last): File /usr/lib/python2.4/site-packages/pymol/__init__.py, line 105, in ? import pymol File /usr/lib/python2.4/site-packages/pymol/__init__.py, line 329, in ? import _cmd ImportError: /usr/lib/python2.4/site-packages/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding can anyone help me to fix this problem? Thanks a lot in advance Christoph * * * * * * * * * * * * * * * * * * Christoph Kaiser TU München Department of Chemistry Biotechnology Laboratory Prof. Dr. Johannes Buchner mail: christoph.kai...@ch.tum.de phone: +49 089 289 13 371 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] PymOl INstallation PRoblems
Hi Nick, This sounds vaguely similar to the msvcr71.dll issues that were recently discussed on the list (searching the list archives will give you more info on this, but the quick fix is to search the hd for msvcr71.dll and copy it to the pymol install directory). If that doesn't resolve the problem, then some more details might be useful. Which version of pymol are you running (I'm assuming one of the recent win32 binary distributions)? Are there any error messages, and if so what do they say? Are you starting-up pymol by clicking the start menu icon (if so, try opening a dos window, going to the pymol directory, and starting from the dos prompt...this probably won't fix the problem, but will probably give more detailed error messages)? The quickest resolution (assuming msvcr71.dll isn't the problem) might be to install a slightly older version. Hope this helps, Pete Hi PyWorld, I have been trying to help a friend install PyMol on her laptop (Sony Vaio) that has Windows XP Home Edition. The installation runs smooth with no problem at all. But once we try to open the program, its seems to stall, then crashes, and Windows XP asks if we would like to send a error report??? I have searched the archives and online for answers, but with no luck. Therefore, I present to you, my PyFriends, our dilemma and seek a remedy to our problem. I give you my word, my good friends, that upon finding the solution, I will not take all the credit for solving this mysteryjust kidding, credit will be duly noted. Thanks in advance for any and all help! Cheers, Nick Pete Meyer Fu Lab BMCB grad student Cornell University
