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From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2021-09-17 22:56:42
|
Dear PyMOL Users mailing list, Today is the last day to register for the SSRL/LCLS User Meeting that starts on Monday. It is free and virtual. https://events.bizzabo.com/SLAC-UsersMeeting-2021/home. The poster session runs 12 - 1 PM Pacific Time M-Th. You use the gathertown software to attend it. Navigation of the poster session is like playing a 1990s computer game. I was on the poster judging team. We spent this week judging the posters virtually. We made our selections of the seven poster prize finalists today. All of the semifinalist posters were excellent. You will see PyMOL put to good use in many posters and talks. Best regards, Blaine, SSRL User Executive Committee member and past chair Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology |
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From: sunyeping <sun...@al...> - 2021-09-15 05:35:29
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Dear Mr. Jarrett, Yes, with the glm of version 0.0.9, pymol can be installed successful. Thank you very much:) ------------------------------------------------------------------ From:Jarrett Johnson <jar...@sc...> Send Time:2021年9月13日(星期一) 01:30 To:孙业平 <sun...@al...> Cc:pymol-users <pym...@li...> 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 <glm/gtc/epsilon.hpp> 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 <pym...@li...> wrote: Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include <glm/ext/vector_relational.hpp>" to "#include <glm/vector_relational.hpp>". 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 <pym...@li...> Send Time:2021年9月12日(星期日) 15:39 To:pymol-users <pym...@li...> 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 <glm/ext/vector_relational.hpp> ^ 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<class T> glm::tvec3<T, (glm::precision)0u> glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3<T, defaultp> 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<float, (glm::precision)0u>’ 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 much of any help. Best regards. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li... Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Jarrett Johnson | Senior Developer [Schrodinger Logo] |
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From: Ecem G. <ece...@gm...> - 2021-09-13 15:58:22
|
Dear all, I have a question regarding the alignment tool of PyMOL. I would like to align the binding sites of two different proteins with each other and get the corresponding RMSD value. To do this, I selected the ligand and then picked the residues within 8 A away from the ligand of interest for both proteins, separately, using action>modify>around>residues within 8 A . Then, I tried to align these two selections using action>align>to selection. However, I got an error stating "ExecutiveAlign: mobile selection must derive from one object only." How can I handle this? I appreciate your feedback. Thanks in advance. Kind regards |
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From: Jarrett J. <jar...@sc...> - 2021-09-12 18:22:13
|
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 <glm/gtc/epsilon.hpp> 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 < pym...@li...> wrote: > Dear all, > > Now I revised Line 4 in the SceneView.cpp file from > "#include <glm/ext/vector_relational.hpp>" to > "#include <glm/vector_relational.hpp>". > 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 <pym...@li...> > Send Time:2021年9月12日(星期日) 15:39 > To:pymol-users <pym...@li...> > 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 <glm/ext/vector_relational.hpp> > ^ > 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<class T> glm::tvec3<T, (glm::precision)0u> glm::make_vec3(const T*) > GLM_FUNC_QUALIFIER tvec3<T, defaultp> 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<float, (glm::precision)0u>’ > > 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 much of any help. > > Best regards. > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> |
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From: sunyeping <sun...@al...> - 2021-09-12 08:40:23
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Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include <glm/ext/vector_relational.hpp>" to "#include <glm/vector_relational.hpp>". 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 <pym...@li...> Send Time:2021年9月12日(星期日) 15:39 To:pymol-users <pym...@li...> 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 <glm/ext/vector_relational.hpp> ^ 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<class T> glm::tvec3<T, (glm::precision)0u> glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3<T, defaultp> 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<float, (glm::precision)0u>’ 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 much of any help. Best regards. |
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From: sunyeping <sun...@al...> - 2021-09-12 07:39:03
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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 <glm/ext/vector_relational.hpp> ^ 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<class T> glm::tvec3<T, (glm::precision)0u> glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3<T, defaultp> 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<float, (glm::precision)0u>’ 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 much of any help. Best regards. |
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From: #JESSICA L. J. <JESSICAJ002@e.ntu.edu.sg> - 2021-08-31 16:41:29
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Dear Joel, Thank you so much for sharing! Totally answered my question, very much appreciated and I will look into the command as well. Thank you very much for your kind guidance and assistance! Jessica Lim From: Joel Tyndall<mailto:joe...@ot...> Sent: Tuesday, 31 August 2021 5:55 am To: #JESSICA LIM JIAYING#<mailto:JESSICAJ002@e.ntu.edu.sg>; pym...@li...<mailto:pym...@li...> Subject: RE: [PyMOL] Recognition and Display of Secondary Structure Cartoon Hi Jessica, Generally secondary structure is extracted from a pdb file and PyMol would read this. e.g. HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 SHEET 1 A 4 GLN A 2 THR A 4 0 SHEET 2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N THR A 96 O ASN B 98 SHEET 4 A 4 GLN B 2 ILE B 3 -1 N ILE B 3 O LEU A 97 Sometimes the pdb file is incomplete or does not display all secondary structure. Using the command dss in Pymol can usually help define/display correct ss. https://www.pymolwiki.org/index.php/Dss Hope this helps J From: #JESSICA LIM JIAYING# <JESSICAJ002@e.ntu.edu.sg> Sent: Saturday, 28 August 2021 6:54 pm To: pym...@li... Subject: [PyMOL] Recognition and Display of Secondary Structure Cartoon Hi all, I am wondering how PyMOL recognises and display secondary structure (like alpha helix) when selecting the ‘Cartoon’ function. I have attached an image of my molecule where only certain regions are displayed in the cartoon representation whereas there is helical propensity throughout my molecule as seen in the image. Hence, how does PyMOL decide on the secondary structure features? Thank you so much! Any suggestions/advice on where to look will be greatly appreciated! Jessica Lim |
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From: Joel T. <joe...@ot...> - 2021-08-30 22:09:48
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Hi Jessica, Generally secondary structure is extracted from a pdb file and PyMol would read this. e.g. HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 SHEET 1 A 4 GLN A 2 THR A 4 0 SHEET 2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N THR A 96 O ASN B 98 SHEET 4 A 4 GLN B 2 ILE B 3 -1 N ILE B 3 O LEU A 97 Sometimes the pdb file is incomplete or does not display all secondary structure. Using the command dss in Pymol can usually help define/display correct ss. https://www.pymolwiki.org/index.php/Dss Hope this helps J From: #JESSICA LIM JIAYING# <JESSICAJ002@e.ntu.edu.sg> Sent: Saturday, 28 August 2021 6:54 pm To: pym...@li... Subject: [PyMOL] Recognition and Display of Secondary Structure Cartoon Hi all, I am wondering how PyMOL recognises and display secondary structure (like alpha helix) when selecting the 'Cartoon' function. I have attached an image of my molecule where only certain regions are displayed in the cartoon representation whereas there is helical propensity throughout my molecule as seen in the image. Hence, how does PyMOL decide on the secondary structure features? Thank you so much! Any suggestions/advice on where to look will be greatly appreciated! Jessica Lim |
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From: #JESSICA L. J. <JESSICAJ002@e.ntu.edu.sg> - 2021-08-28 07:29:12
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Hi all, I am wondering how PyMOL recognises and display secondary structure (like alpha helix) when selecting the ‘Cartoon’ function. I have attached an image of my molecule where only certain regions are displayed in the cartoon representation whereas there is helical propensity throughout my molecule as seen in the image. Hence, how does PyMOL decide on the secondary structure features? Thank you so much! Any suggestions/advice on where to look will be greatly appreciated! Jessica Lim |
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From: Gonzalo R. <go...@pr...> - 2021-08-17 00:18:05
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Hi all,
I am trying to make a python function that mutates a residue and selects
the rotamer with the lowest energy. Here is what I have so far:
# Initialize, load your Protein
cmd.wizard("mutagenesis")
cmd.load(pdb_file)
cmd.do("refresh_wizard", echo=0)
# Mutate residue res_num to res_type
cmd.get_wizard().do_select(res_num)
cmd.get_wizard().set_mode(res_type)
# Select the rotamer with the lowest energy (MODIFY HERE)
cmd.frame(lowest_energy_rotamer)
# Apply the mutation
cmd.get_wizard().apply()
Thank you so much in advance, any tips and tricks are greatly appreciated.
Sincerely,
Gonzalo Rubio
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From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2021-08-16 15:02:21
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Hi Mo, I apologize. I did not fully address your question the first time. In the internal gui on the right, click on the 'A' menu of the (interface) selection. Select "extract to object" or "copy to object". The new object called "obj1" can be saved to a cif file by selecting it while using "Export molecule" under the File pulldown. Alternatively, enter on the command line: save obj1.cif, obj1 You can save it to a PDBd file by simply changing the file extension to pdb. Best regards, Blaine ________________________________________ From: Mohammad Goodarzi [moh...@gm...] Sent: Monday, August 16, 2021 9:19 AM To: Mooers, Blaine H.M. (HSC) Cc: pym...@li... Subject: Re: [EXTERNAL] [PyMOL] extract interference residue Hi Blaine, How can I extract them? do you know ? Thanks Mo On Sun, Aug 15, 2021 at 5:42 PM Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> wrote: Hi Mohammad, I can confirm that the interfaceResidues.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__interfaceResidues.py&d=DwQFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=Q5cq0vYNIh7OQ34lxJLMnsiit0p4PTVIv14ivaZ0cCE&s=Ii_pYmlADVqhxAchp82tnBCym3X5l89ANiXnV24jhOI&e=> script works in PyMOL version 1.5.2 running with Python3.8 on Mac OS 10.15.7. You did not find interface residues in 1ak4 because chains A and B are more than 15 Angstroms apart. They have no direct interactions and hence have no interface. The first rule in troubleshooting PyMOL is to display and inspect the structure in the viewport to check your assumptions about the structure. However, chains C and D are close enough to interact. The following command uses the interfaceResidue() function to create an interface object called "interface" that includes all of the interacting residues between chains C and D. interfaceResidues("1ak4", cA="c. C", cB="c. D", cutoff=1.0, selName="interface") You do not need to use 'foundResidues =' to create another object. In addition, cA in your command should be set equal to "c. A". The c. is an abbreviation for "chain". Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC<https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC> (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ou.edu_structuralbiology&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=Q5cq0vYNIh7OQ34lxJLMnsiit0p4PTVIv14ivaZ0cCE&s=B15Mz_0x7gGI17o6LD8bBPswQ-uyRIMbCfUc-trD5No&e=> ________________________________________ From: Mohammad Goodarzi [moh...@gm...<mailto:moh...@gm...>] Sent: Sunday, August 15, 2021 3:24 PM To: pym...@li...<mailto:pym...@li...> Subject: [EXTERNAL] [PyMOL] extract interference residue Hello Guys, I am trying to extract the interference residue from a given protein PDB. I have a protein named 1ak4 which has two chain A and B. I open pymol, then go to file, the run the script from here https://pymolwiki.org/index.php/InterfaceResidues#Simple_Example<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_InterfaceResidues-23Simple-5FExample&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=Q5cq0vYNIh7OQ34lxJLMnsiit0p4PTVIv14ivaZ0cCE&s=d_61y5nDwbx4-WMZXUiaHEcOTRtCXvyV0MuqW4WJGgU&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_InterfaceResidues-23Simple-5FExample&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=g8YHyNiGloFOsn1txDr06UZPT4xLrbEx0oH4IhUeltQ&s=_yZQI3Y7rTf4JHXGuW5ZmZIG4qSLy9d5L6PLbJ20VcM&e=> Then I run the following command which gives me error foundResidues = interfaceResidues("1ak4", cA="B", cB="B", cutoff=0.75, selName="foundIn1QOX") Could someone tell me how to identify the interference residue and extract it from pymol? Thanks Mo |
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From: Mohammad G. <moh...@gm...> - 2021-08-16 14:19:39
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Hi Blaine,
How can I extract them? do you know ?
Thanks
Mo
On Sun, Aug 15, 2021 at 5:42 PM Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:
> Hi Mohammad,
>
> I can confirm that the interfaceResidues.py script works in PyMOL version
> 1.5.2 running with Python3.8 on Mac OS 10.15.7.
>
> You did not find interface residues in 1ak4 because chains A and B are
> more than 15 Angstroms apart.
> They have no direct interactions and hence have no interface. The first
> rule in troubleshooting
> PyMOL is to display and inspect the structure in the viewport to check
> your assumptions about the structure.
>
> However, chains C and D are close enough to interact. The following
> command uses the
> interfaceResidue() function to create an interface object called
> "interface" that includes
> all of the interacting residues between chains C and D.
>
> interfaceResidues("1ak4", cA="c. C", cB="c. D", cutoff=1.0,
> selName="interface")
>
> You do not need to use 'foundResidues =' to create another object.
> In addition, cA in your command should be set equal to "c. A".
> The c. is an abbreviation for "chain".
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC
> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC>
> (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ________________________________________
> From: Mohammad Goodarzi [moh...@gm...]
> Sent: Sunday, August 15, 2021 3:24 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] extract interference residue
>
> Hello Guys,
>
> I am trying to extract the interference residue from a given protein PDB.
> I have a protein named 1ak4 which has two chain A and B.
>
> I open pymol, then go to file, the run the script from here
> https://pymolwiki.org/index.php/InterfaceResidues#Simple_Example<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_InterfaceResidues-23Simple-5FExample&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=g8YHyNiGloFOsn1txDr06UZPT4xLrbEx0oH4IhUeltQ&s=_yZQI3Y7rTf4JHXGuW5ZmZIG4qSLy9d5L6PLbJ20VcM&e=
> >
>
>
> Then I run the following command which gives me error
>
>
> foundResidues = interfaceResidues("1ak4", cA="B", cB="B", cutoff=0.75,
> selName="foundIn1QOX")
>
> Could someone tell me how to identify the interference residue and extract
> it from pymol?
>
> Thanks
> Mo
>
|
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From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2021-08-15 23:22:20
|
Hi Mohammad,
I can confirm that the interfaceResidues.py script works in PyMOL version 1.5.2 running with Python3.8 on Mac OS 10.15.7.
You did not find interface residues in 1ak4 because chains A and B are more than 15 Angstroms apart.
They have no direct interactions and hence have no interface. The first rule in troubleshooting
PyMOL is to display and inspect the structure in the viewport to check your assumptions about the structure.
However, chains C and D are close enough to interact. The following command uses the
interfaceResidue() function to create an interface object called "interface" that includes
all of the interacting residues between chains C and D.
interfaceResidues("1ak4", cA="c. C", cB="c. D", cutoff=1.0, selName="interface")
You do not need to use 'foundResidues =' to create another object.
In addition, cA in your command should be set equal to "c. A".
The c. is an abbreviation for "chain".
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center
Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312
Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Mohammad Goodarzi [moh...@gm...]
Sent: Sunday, August 15, 2021 3:24 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] extract interference residue
Hello Guys,
I am trying to extract the interference residue from a given protein PDB. I have a protein named 1ak4 which has two chain A and B.
I open pymol, then go to file, the run the script from here https://pymolwiki.org/index.php/InterfaceResidues#Simple_Example<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_InterfaceResidues-23Simple-5FExample&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=g8YHyNiGloFOsn1txDr06UZPT4xLrbEx0oH4IhUeltQ&s=_yZQI3Y7rTf4JHXGuW5ZmZIG4qSLy9d5L6PLbJ20VcM&e=>
Then I run the following command which gives me error
foundResidues = interfaceResidues("1ak4", cA="B", cB="B", cutoff=0.75, selName="foundIn1QOX")
Could someone tell me how to identify the interference residue and extract it from pymol?
Thanks
Mo
|
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From: Mohammad G. <moh...@gm...> - 2021-08-15 20:25:03
|
Hello Guys, I am trying to extract the interference residue from a given protein PDB. I have a protein named 1ak4 which has two chain A and B. I open pymol, then go to file, the run the script from here https://pymolwiki.org/index.php/InterfaceResidues#Simple_Example Then I run the following command which gives me error foundResidues = interfaceResidues("1ak4", cA="B", cB="B", cutoff=0.75, selName="foundIn1QOX") Could someone tell me how to identify the interference residue and extract it from pymol? Thanks Mo |
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From: Shipra B. <shi...@gm...> - 2021-08-15 15:16:13
|
Hi Everyone, I have a structure of protein ligand complex generated using CCP4. While trying to load the mmcif file of the structure , I am getting this warning *mmCIF- Warning: no coordinates found in data_comp_list* *mmCIF- Warning: no coordinates found in data_comp_DRG* The structure has two ligands represented by DRG. Looks like there is some problem in linking the ligand dictionary information with its coordinates. Looking forward to any suggestion. Thanks, Renu |
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From: Neena S. E. <nee...@gm...> - 2021-07-27 21:10:11
|
Thank you Jarrett, that works very well!
On Tue, 27 Jul 2021 at 12:54, Jarrett Johnson <
jar...@sc...> wrote:
> The following command is issued when you click on GUI:
>
> cmd.zoom('center', i, animate=-1)
>
> or
>
> zoom center, i, animate=-1
>
> where "i" would be 15 in your case.
>
> On Tue, Jul 27, 2021 at 10:56 AM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hello PyMOL users,
>>
>> In addition to the current PyMOL interface for zoom settings (shown
>> below), is there a command to get a zoom setting like say 15 Angstrom
>> sphere?
>>
>> [image: image.png]
>> Many thanks,
>> Neena
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>
|
|
From: Jarrett J. <jar...@sc...> - 2021-07-27 16:54:26
|
The following command is issued when you click on GUI:
cmd.zoom('center', i, animate=-1)
or
zoom center, i, animate=-1
where "i" would be 15 in your case.
On Tue, Jul 27, 2021 at 10:56 AM Neena Susan Eappen <nee...@gm...>
wrote:
> Hello PyMOL users,
>
> In addition to the current PyMOL interface for zoom settings (shown
> below), is there a command to get a zoom setting like say 15 Angstrom
> sphere?
>
> [image: image.png]
> Many thanks,
> Neena
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
--
*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>
|
|
From: Neena S. E. <nee...@gm...> - 2021-07-27 14:53:51
|
Hello PyMOL users, In addition to the current PyMOL interface for zoom settings (shown below), is there a command to get a zoom setting like say 15 Angstrom sphere? [image: image.png] Many thanks, Neena |
|
From: Neena S. E. <nee...@gm...> - 2021-07-25 23:08:27
|
Thank you Qiang Chen, Criss Hartzell and Adam Steinberg for your insights on this data processing issue. Regards, Neena On Sat, 24 Jul 2021 at 12:13, H. Adam Steinberg <h.a...@gm...> wrote: > Hi Neena, > > When you render out of PyMOL using the button (not the command line), it > just renders out the view window. Therefore if you make the helix fill the > entire viewport rectangle, you will effectively render out a ‘cropped” > image. > > If you turn on transparency (in the background setting), you will no > longer have a background to worry about as PyMOL will render just the helix > on transparency. > > Adam > > On Jul 23, 2021, at 11:57 AM, Neena Susan Eappen <nee...@gm...> > wrote: > > Hello PyMOL users, > > Let me clarify my question. Shown below is one example figure. There is no > way to crop any images on Origin graphing software. For this figure, I > cropped PyMOL peptide image files on word document and then inserted in > Origin graph. This is time consuming. > Is there a way to crop on PyMOL? > > <image.png> > Any insight would be appreciated, > > Thank you, Neena > > On Jul 22, 2021, at 5:43 PM, Neena Susan Eappen <nee...@gm...> > wrote: > > Hello PyMOL users, > > I have some issues exporting images from PyMOL into a data analysis > software called OriginLab (https://www.originlab.com/). If there is > anyone in this mail list who integrates figures from PyMOL into Origin, > please email me. I need some insights for data representation. > > Many thanks, > Neena > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > |
|
From: H. A. S. <h.a...@gm...> - 2021-07-24 16:14:05
|
Hi Neena, When you render out of PyMOL using the button (not the command line), it just renders out the view window. Therefore if you make the helix fill the entire viewport rectangle, you will effectively render out a ‘cropped” image. If you turn on transparency (in the background setting), you will no longer have a background to worry about as PyMOL will render just the helix on transparency. Adam > On Jul 23, 2021, at 11:57 AM, Neena Susan Eappen <nee...@gm...> wrote: > > Hello PyMOL users, > > Let me clarify my question. Shown below is one example figure. There is no way to crop any images on Origin graphing software. For this figure, I cropped PyMOL peptide image files on word document and then inserted in Origin graph. This is time consuming. > Is there a way to crop on PyMOL? > > <image.png> > Any insight would be appreciated, > > Thank you, Neena > > On Jul 22, 2021, at 5:43 PM, Neena Susan Eappen <nee...@gm... <mailto:nee...@gm...>> wrote: > >> Hello PyMOL users, >> >> I have some issues exporting images from PyMOL into a data analysis software called OriginLab (https://www.originlab.com/ <https://www.originlab.com/>). If there is anyone in this mail list who integrates figures from PyMOL into Origin, please email me. I need some insights for data representation. >> >> Many thanks, >> Neena > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
|
From: Chen, Q. <qi...@pi...> - 2021-07-23 17:54:25
|
I often process the images from pymol or originLab in GIMP or photoshop. You could set the pixel content of your pymol image, Png - PyMOLWiki<https://pymolwiki.org/index.php/Png>. But I guess this is not the "crop" you expect. Best, Charles Png - PyMOLWiki<https://pymolwiki.org/index.php/Png> Comments Transparent Backgrounds. Use the `ray_opaque_background` setting to output images with transparent backgrounds. set ray_opaque_background, 0 This can be useful for presentations, images that are placed on top of a background of nonuniform color (e.g. gradients), and images that overlap text or other images. pymolwiki.org ________________________________ From: pym...@li... <pym...@li...> Sent: Friday, July 23, 2021 12:57 PM To: pym...@li... <pym...@li...> Subject: PyMOL-users Digest, Vol 182, Issue 12 Send PyMOL-users mailing list submissions to pym...@li... To subscribe or unsubscribe via the World Wide Web, visit https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=04%7C01%7Cqic8%40pitt.edu%7Cc9a0e7b479624314837e08d94dfaf736%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637626562553080025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9IaE4slS4EFBG%2Fz9onK%2FY6rtKceWLASxgafoQNb2BiU%3D&reserved=0 or, via email, send a message with subject or body 'help' to pym...@li... You can reach the person managing the list at pym...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. Re: Exporting data from PyMOL into OriginLab (Neena Susan Eappen) ---------------------------------------------------------------------- Message: 1 Date: Fri, 23 Jul 2021 12:57:12 -0400 From: Neena Susan Eappen <nee...@gm...> To: pymol-users <pym...@li...> Subject: Re: [PyMOL] Exporting data from PyMOL into OriginLab Message-ID: <C5B...@gm...> Content-Type: text/plain; charset="us-ascii" Hello PyMOL users, Let me clarify my question. Shown below is one example figure. There is no way to crop any images on Origin graphing software. For this figure, I cropped PyMOL peptide image files on word document and then inserted in Origin graph. This is time consuming. Is there a way to crop on PyMOL? Any insight would be appreciated, Thank you, Neena > On Jul 22, 2021, at 5:43 PM, Neena Susan Eappen <nee...@gm...> wrote: > > Hello PyMOL users, > > I have some issues exporting images from PyMOL into a data analysis software called OriginLab (https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.originlab.com%2F&data=04%7C01%7Cqic8%40pitt.edu%7Cc9a0e7b479624314837e08d94dfaf736%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637626562553080025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2NjvYl4IspmqHt5n46tFLMwKEaFTFsNxNIt7ElII81Q%3D&reserved=0). If there is anyone in this mail list who integrates figures from PyMOL into Origin, please email me. I need some insights for data representation. > > Many thanks, > Neena -------------- next part -------------- An HTML attachment was scrubbed... -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 111385 bytes Desc: not available ------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ PyMOL-users mailing list PyM...@li... https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=04%7C01%7Cqic8%40pitt.edu%7Cc9a0e7b479624314837e08d94dfaf736%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637626562553080025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9IaE4slS4EFBG%2Fz9onK%2FY6rtKceWLASxgafoQNb2BiU%3D&reserved=0 Unsubscribe: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=04%7C01%7Cqic8%40pitt.edu%7Cc9a0e7b479624314837e08d94dfaf736%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637626562553080025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=t8Uumr9EXcb2wGkQ%2FdYfC9bxnhM6JyQY%2BYZKkXpAZAk%3D&reserved=0 ------------------------------ End of PyMOL-users Digest, Vol 182, Issue 12 ******************************************** |
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From: Neena S. E. <nee...@gm...> - 2021-07-23 16:57:26
|
Hello PyMOL users, Let me clarify my question. Shown below is one example figure. There is no way to crop any images on Origin graphing software. For this figure, I cropped PyMOL peptide image files on word document and then inserted in Origin graph. This is time consuming. Is there a way to crop on PyMOL? Any insight would be appreciated, Thank you, Neena > On Jul 22, 2021, at 5:43 PM, Neena Susan Eappen <nee...@gm...> wrote: > > Hello PyMOL users, > > I have some issues exporting images from PyMOL into a data analysis software called OriginLab (https://www.originlab.com/). If there is anyone in this mail list who integrates figures from PyMOL into Origin, please email me. I need some insights for data representation. > > Many thanks, > Neena |
|
From: Neena S. E. <nee...@gm...> - 2021-07-22 21:44:16
|
Hello PyMOL users, I have some issues exporting images from PyMOL into a data analysis software called OriginLab (https://www.originlab.com/). If there is anyone in this mail list who integrates figures from PyMOL into Origin, please email me. I need some insights for data representation. Many thanks, Neena |
|
From: Jarrett J. <jar...@sc...> - 2021-07-22 18:29:49
|
Good afternoon, After some email exchanges with Ursula and Luca, we were able to confirm that this issue is caused on Macs when you open PyMOL with a session file rather than opening a session file within PyMOL itself. For a workaround if you do observe this issue, it seems that providing: `set use_shaders, on` will restore the UI font to the proper size. I'll aim to have this addressed with the upcoming 2.5.2 maintenance release. Thanks, Jarrett J On Tue, Jul 20, 2021 at 9:26 PM Ursula Schulze-Gahmen via PyMOL-users < pym...@li...> wrote: > I know this has been asked before, but > for older versions of pymol. > I just updated my pymol version to 2.5 by installing from sbgrid. I > installed on a Macbook Pro using OSX 10.15.7. The font size in the GUI is > extremely small now and I cannot find a setting to change this to a > readable size. > Any suggestions on how to change this? > > Thanks > > Ursula > -- > Ursula Schulze-Gahmen, PhD > Staff Research Scientist > The J David Gladstone Institutes > 1650 Owens St. > San Francisco, CA 94158 > (415) 734 4835 > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> |
|
From: Ursula Schulze-G. <urs...@gl...> - 2021-07-21 01:25:58
|
I know this has been asked before, but for older versions of pymol. I just updated my pymol version to 2.5 by installing from sbgrid. I installed on a Macbook Pro using OSX 10.15.7. The font size in the GUI is extremely small now and I cannot find a setting to change this to a readable size. Any suggestions on how to change this? Thanks Ursula -- Ursula Schulze-Gahmen, PhD Staff Research Scientist The J David Gladstone Institutes 1650 Owens St. San Francisco, CA 94158 (415) 734 4835 |
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