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  • Molekel - Message forums

    Discussion forums: Open Discussion

    Expanded view | Monitor forum | Save place

    Welcome to Open Discussion
    Submitted by Unset; posted on Wednesday, September 13, 2006
    Welcome to Open Discussion
    New User Problem
    Submitted by Christopher Barry; posted on Friday, February 16, 2007
    Hello, I just installed the latest binary of molekel_5 and am not able to get many features to work. I opened a molecule (pdb) and cannot generate any surfaces. I can get the menu to open but all features are faded out. Is this because I have not installed some necessary accessory application? Thanks
    New User Problem
    Submitted by Christopher Barry; posted on Friday, February 16, 2007
    Hello, I just installed the latest binary of molekel_5 and am not able to get many features to work. I opened a molecule (pdb) and cannot generate any surfaces. I can get the menu to open but all features are faded out. Is this because I have not installed some necessary accessory application? Thanks
    Re: New User Problem
    Submitted by Ugo Varetto; posted on Monday, March 05, 2007
    The type of surfaces that can be generated depends on the data read from the file. * SAS/VdW surfaces can be generated for molecules read from any file format (including PDBs). * SES (Connolly) can be generated as point clouds and as regular surfaces by specifying the path to M.F. Sanner's msms executable. * Surfaces from grid data can be generated from Gaussian .cube files only (and ADF tape 41 file if you compile a version from the code in the vault). * Surfaces from electron density data can be generated only if the proper information is specified in the file; Gaussian, GAMESS and Molden formats may contain this information. To generate a surface a molecule needs of course to be selected first.
    Re: New User Problem
    Submitted by B Plank; posted on Tuesday, May 15, 2007
    "Surfaces from grid data can be generated from Gaussian .cube files only (and ADF tape 41 file if you compile a version from the code in the vault)." Can you please let me know how to compile a version from the code in the vault? I would like to visualize the orbitals from adf *t41 files. Thanks
    Re: New User Problem
    Submitted by Ugo Varetto; posted on Friday, June 08, 2007
    Version 5.1.1 released on May 11 has some support for ADF tape41 files.
    Re: New User Problem
    Submitted by yang Si-Ya; posted on Sunday, September 06, 2009
    Hi, I cann't change atoms color used molekel 5.4 or 5.3 I request to adjust each atom colors for a *xyz format file in accordance with my preforence. Best resgards. Yang si-ya
    Molekel 5.x request
    Submitted by Lee Richter; posted on Saturday, April 28, 2007
    Not sure this is the right place to post a request but... I have been a 'religous' user of Molekel 4.3 for visualization of vibrations from Gaussian calculations. In general, I find it superior to Molden and Agui for that specific function. I'd like to suggest/request improvements in the new Molekel (tis way cool) with regard to this aspect of the program (which seem to not of caught up to it's older brother) Please include both the vibration number and the IR intensity in the vibration choice list (along with th frequency and symmetry). Please 'leave' the arrows displayed on when the animation is stopped Thanks very much -Lee
    Re: Molekel 5.x request
    Submitted by Ugo Varetto; posted on Friday, June 08, 2007
    Hi, thanks for the feedback; in future versions it will be possible to pause the animation and see the arrows when the animation is paused; this can actually be done today by disabling animation into the animation dialog but we definitely need a pause button. Also note that the display of arrows in Molekel 4.3 is wrong because arrows always point in the same direction so if you take a snapshot chances are that the atom is actually moving in the direction opposite to the one shown by the arrow. It should be easy to add vibration number and IR intensity...will check.
    build error
    Submitted by Taner E. Dirama; posted on Tuesday, July 24, 2007
    I have been trying to build molekel 5.2 from the source. I am getting linking errors at the final stage during building of the executable. Any ideas? The installation is on a x86_64 with redhat enterprise linux 5. The error log and the contents of the CMakeCache.txt are below. Thanks, -Taner -- error.log ---------------------------------------------------- [diramate@blue build]$ make [ 1%] Generating moc_EventPositionTimeWidget.cxx [ 2%] Generating moc_MainWindow.cxx [ 3%] Generating moc_MoleculeRenderingStyleWidget.cxx [ 4%] Generating moc_WorkspaceTreeWidget.cxx [ 5%] Generating moc_MoleculeVibrationWidget.cxx [ 6%] Generating moc_MoleculeTrajectoryWidget.cxx [ 7%] Generating moc_MoleculeAnimationModeWidget.cxx [ 8%] Generating moc_TimeStepWidget.cxx [ 9%] Generating moc_MoleculeElDensSurfaceWidget.cxx [ 10%] Generating moc_ImagePlaneProbeWidget.cxx [ 11%] Generating moc_GridDataSurfaceWidget.cxx [ 12%] Generating moc_SasWidget.cxx [ 13%] Generating moc_SesWidget.cxx [ 14%] Generating moc_ViewPropertiesWidget.cxx [ 15%] Generating moc_ShaderWidget.cxx [ 16%] Generating moc_MoleculeAnimationDialog.cxx [ 17%] Generating moc_TimeStepDialog.cxx [ 18%] Generating moc_ComputeElDensSurfaceDialog.cxx [ 19%] Generating moc_ImagePlaneProbeDialog.cxx [ 20%] Generating moc_GridDataSurfaceDialog.cxx [ 21%] Generating moc_ExportAnimationDialog.cxx [ 22%] Generating moc_SasDialog.cxx [ 23%] Generating moc_SesDialog.cxx [ 24%] Generating moc_ShadersDialog.cxx [ 25%] Generating moc_EventFilter.cxx [ 26%] Generating moc_EventPlayer.cxx [ 27%] Generating moc_EventRecorderWidget.cxx [ 28%] Generating moc_EventPlayerWidget.cxx [ 29%] Generating moc_QGLSLShaderEditorWidget.cxx Scanning dependencies of target Molekel [ 29%] Building CXX object CMakeFiles/Molekel.dir/versioninfo.o [ 30%] Building CXX object CMakeFiles/Molekel.dir/main.o [ 31%] Building CXX object CMakeFiles/Molekel.dir/MainWindow.o [ 32%] Building CXX object CMakeFiles/Molekel.dir/MolekelMolecule.o [ 33%] Building CXX object CMakeFiles/Molekel.dir/MolekelData.o [ 34%] Building CXX object CMakeFiles/Molekel.dir/old/molekeltypes.o [ 35%] Building CXX object CMakeFiles/Molekel.dir/old/readgauss.o [ 36%] Building CXX object CMakeFiles/Molekel.dir/old/readgamess.o [ 37%] Building CXX object CMakeFiles/Molekel.dir/old/calcdens.o [ 38%] Building CXX object CMakeFiles/Molekel.dir/old/utilities.o [ 39%] Building CXX object CMakeFiles/Molekel.dir/old/readmolden.o [ 40%] Building CXX object CMakeFiles/Molekel.dir/resources/icon.o [ 41%] Building CXX object CMakeFiles/Molekel.dir/resources/atomsdata.o [ 42%] Building CXX object CMakeFiles/Molekel.dir/resources/license.o [ 43%] Building CXX object CMakeFiles/Molekel.dir/utility/CommandLine.o [ 44%] Building CXX object CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o [ 45%] Building CXX object CMakeFiles/Molekel.dir/utility/MolekelChemPDBImporter.o [ 46%] Building CXX object CMakeFiles/Molekel.dir/utility/BabelToMOIV.o [ 47%] Building CXX object CMakeFiles/Molekel.dir/utility/vtkMSMSReader.o [ 48%] Building CXX object CMakeFiles/Molekel.dir/utility/System.o [ 49%] Building CXX object CMakeFiles/Molekel.dir/utility/OBMSMSFormat.o [ 50%] Building CXX object CMakeFiles/Molekel.dir/utility/ElementTable.o [ 51%] Building CXX object CMakeFiles/Molekel.dir/utility/MolekelToOpenBabel.o [ 52%] Building CXX object CMakeFiles/Molekel.dir/utility/OBMoldenFormat.o [ 53%] Building CXX object CMakeFiles/Molekel.dir/utility/OBZmatrixFormat.o [ 54%] Building CXX object CMakeFiles/Molekel.dir/utility/OBT41Format.o [ 55%] Building CXX object CMakeFiles/Molekel.dir/utility/events/ObjectName.o [ 56%] Building CXX object CMakeFiles/Molekel.dir/utility/events/EventPlayer.o [ 57%] Building CXX object CMakeFiles/Molekel.dir/utility/events/EventRecorderWidget.o [ 58%] Building CXX object CMakeFiles/Molekel.dir/utility/events/EventPlayerWidget.o [ 59%] Building CXX object CMakeFiles/Molekel.dir/utility/vtkGLSLShaderActor.o [ 60%] Building CXX object CMakeFiles/Molekel.dir/utility/shaders/Shaders.o [ 61%] Building CXX object CMakeFiles/Molekel.dir/utility/shaders/ShaderParameters.o [ 62%] Building CXX object CMakeFiles/Molekel.dir/utility/shaders/QGLSLShaderEditorWidget.o [ 63%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeRenderingStyleWidget.o [ 64%] Building CXX object CMakeFiles/Molekel.dir/widgets/WorkspaceTreeWidget.o [ 65%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeVibrationWidget.o [ 66%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeTrajectoryWidget.o [ 67%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeAnimationModeWidget.o [ 68%] Building CXX object CMakeFiles/Molekel.dir/widgets/TimeStepWidget.o [ 69%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeElDensSurfaceWidget.o [ 70%] Building CXX object CMakeFiles/Molekel.dir/widgets/ImagePlaneProbeWidget.o [ 71%] Building CXX object CMakeFiles/Molekel.dir/widgets/GridDataSurfaceWidget.o [ 72%] Building CXX object CMakeFiles/Molekel.dir/moc_MainWindow.o [ 73%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeRenderingStyleWidget.o [ 74%] Building CXX object CMakeFiles/Molekel.dir/moc_WorkspaceTreeWidget.o [ 75%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeVibrationWidget.o [ 76%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeTrajectoryWidget.o [ 77%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeAnimationModeWidget.o [ 78%] Building CXX object CMakeFiles/Molekel.dir/moc_TimeStepWidget.o [ 79%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeElDensSurfaceWidget.o [ 80%] Building CXX object CMakeFiles/Molekel.dir/moc_ImagePlaneProbeWidget.o [ 81%] Building CXX object CMakeFiles/Molekel.dir/moc_GridDataSurfaceWidget.o [ 82%] Building CXX object CMakeFiles/Molekel.dir/moc_SasWidget.o [ 83%] Building CXX object CMakeFiles/Molekel.dir/moc_SesWidget.o [ 84%] Building CXX object CMakeFiles/Molekel.dir/moc_ViewPropertiesWidget.o [ 85%] Building CXX object CMakeFiles/Molekel.dir/moc_ShaderWidget.o [ 86%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeAnimationDialog.o [ 87%] Building CXX object CMakeFiles/Molekel.dir/moc_TimeStepDialog.o [ 88%] Building CXX object CMakeFiles/Molekel.dir/moc_ComputeElDensSurfaceDialog.o [ 89%] Building CXX object CMakeFiles/Molekel.dir/moc_ImagePlaneProbeDialog.o [ 90%] Building CXX object CMakeFiles/Molekel.dir/moc_GridDataSurfaceDialog.o [ 91%] Building CXX object CMakeFiles/Molekel.dir/moc_ExportAnimationDialog.o [ 92%] Building CXX object CMakeFiles/Molekel.dir/moc_SasDialog.o [ 93%] Building CXX object CMakeFiles/Molekel.dir/moc_SesDialog.o [ 94%] Building CXX object CMakeFiles/Molekel.dir/moc_ShadersDialog.o [ 95%] Building CXX object CMakeFiles/Molekel.dir/moc_EventFilter.o [ 96%] Building CXX object CMakeFiles/Molekel.dir/moc_EventPlayer.o [ 97%] Building CXX object CMakeFiles/Molekel.dir/moc_EventRecorderWidget.o [ 98%] Building CXX object CMakeFiles/Molekel.dir/moc_EventPlayerWidget.o [ 99%] Building CXX object CMakeFiles/Molekel.dir/moc_QGLSLShaderEditorWidget.o [100%] Building CXX object CMakeFiles/Molekel.dir/moc_EventPositionTimeWidget.o Linking CXX executable dist/bin/Molekel CMakeFiles/Molekel.dir/utility/System.o: In function `GetTemporaryFileName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': System.cpp:(.text+0x3ae): warning: the use of `tmpnam' is dangerous, better use `mkstemp' CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)': OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat15WriteChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::WriteChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)' CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)': OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat14ReadChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::ReadChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flMakeCurrentFont' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flDestroyFont' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flGetCurrentContext' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flGetCurrentFont' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flSetHint' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flCreateFont' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flCreateContext' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flGetBitmap' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flFreeBitmap' /apps/molekel_related/OpenMOIV.src.1.0.3/ undefined reference to `flMakeCurrentContext' collect2: ld returned 1 exit status make[2]: *** [dist/bin/Molekel] Error 1 make[1]: *** [CMakeFiles/Molekel.dir/all] Error 2 make: *** [all] Error 2 -- CMakeCache.txt --------------------------------------------------------- # This is the CMakeCache file. # For build in directory: /apps/molekel_src_5.2/build # It was generated by CMake: /apps/molekel_related/cmake-2.4.6-Linux-i386/bin/cmake # You can edit this file to change values found and used by cmake. # If you do not want to change any of the values, simply exit the editor. # If you do want to change a value, simply edit, save, and exit the editor. # The syntax for the file is as follows: # KEY:TYPE=VALUE # KEY is the name of a variable in the cache. # TYPE is a hint to GUI's for the type of VALUE, DO NOT EDIT TYPE!. # VALUE is the current value for the KEY. ######################## # EXTERNAL cache entries ######################## //Path to a program. CMAKE_AR:FILEPATH=/usr/bin/ar //For backwards compatibility, what version of CMake commands and // syntax should this version of CMake allow. CMAKE_BACKWARDS_COMPATIBILITY:STRING=2.4 //Choose the type of build, options are: None(CMAKE_CXX_FLAGS or // CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel. // CMAKE_BUILD_TYPE:STRING= //Enable/Disable color output during build. CMAKE_COLOR_MAKEFILE:BOOL=ON //CXX compiler. CMAKE_CXX_COMPILER:FILEPATH=/usr/local/bin/g++ //Flags used by the compiler during all build types. CMAKE_CXX_FLAGS:STRING=-L /usr/local/lib64 //Flags used by the compiler during debug builds. CMAKE_CXX_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release minsize builds. CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds (/MD /Ob1 /Oi // /Ot /Oy /Gs will produce slightly less optimized but smaller // files). CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during Release with Debug Info builds. // CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g //C compiler. CMAKE_C_COMPILER:FILEPATH=/usr/local/bin/gcc //Flags for C compiler. CMAKE_C_FLAGS:STRING=' ' //Flags used by the compiler during debug builds. CMAKE_C_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release minsize builds. CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds (/MD /Ob1 /Oi // /Ot /Oy /Gs will produce slightly less optimized but smaller // files). CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during Release with Debug Info builds. // CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g //Flags used by the linker. CMAKE_EXE_LINKER_FLAGS:STRING= //Flags used by the linker during debug builds. CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. // CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Install path prefix, prepended onto install directories. CMAKE_INSTALL_PREFIX:PATH=/usr/local //Path to a program. CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/gmake //Flags used by the linker during the creation of modules. CMAKE_MODULE_LINKER_FLAGS:STRING= //Flags used by the linker during debug builds. CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. // CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Path to a program. 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CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE //Single output directory for building all executables. EXECUTABLE_OUTPUT_PATH:PATH= //GLEW include dir GLEW_INCLUDE_DIR:PATH=/apps/glew/include //GLEW link dir GLEW_LINK_DIR:PATH=/apps/glew/lib //Use OpenInventor dynamic library IV_DYNAMIC:BOOL=ON //OpenInventor/Coin include directory IV_INCLUDE_DIR:PATH=/usr/local/include //OpenInventor/Coin lib directory IV_LINK_DIR:PATH=/usr/local/lib //Single output directory for building all libraries. LIBRARY_OUTPUT_PATH:PATH= //Molekel Qt moc headers MOC_HEADER_FILES:PATH=molekel_moc_headers.cmake //Use OpenMOIV dynamic library MOIV_DYNAMIC:BOOL=ON //OpenMOIV installation directory MOIV_INCLUDE_DIR:PATH=/apps/molekel_related/OpenMOIV.src.1.0.3/include //OpenMOIV installation directory MOIV_LINK_DIR:PATH=/apps/molekel_related/OpenMOIV.src.1.0.3 //Molekel source file list MOLEKEL_SRCS:PATH=molekel_sources.cmake //Value Computed by CMake Molekel_BINARY_DIR:STATIC=/apps/molekel_src_5.2/build //Value Computed by CMake Molekel_SOURCE_DIR:STATIC=/apps/molekel_src_5.2/src //OpenBabel include directory OPENBABEL_INCLUDE_DIR:PATH=/apps/molekel_related/openbabel-2.1.1/include //OpenBabel lib directory OPENBABEL_LINK_DIR:PATH=/apps/molekel_related/openbabel-2.1.1/src //Path to a file. OPENGL_INCLUDE_DIR:PATH=/usr/include //Path to a library. OPENGL_gl_LIBRARY:FILEPATH=/usr/lib64/ //Path to a library. OPENGL_glu_LIBRARY:FILEPATH=/usr/lib64/ //Path to a file. OPENGL_xmesa_INCLUDE_DIR:PATH=/usr/include //The location of the Qt docs QT_DOC_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/doc //Path to a library. QT_FONTCONFIG_LIBRARY:FILEPATH=/usr/lib64/ //Path to a library. QT_FREETYPE_LIBRARY:FILEPATH=/usr/lib64/ //Missing description QT_INCLUDE_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/include //Qt library dir QT_LIBRARY_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/lib //The location of the Qt mkspecs QT_MKSPECS_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/mkspecs //The moc executable QT_MOC_EXECUTABLE:FILEPATH=/usr/local/Trolltech/Qt-4.3.0/bin/moc //The location of the Qt plugins QT_PLUGINS_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/plugins //Path to a library. QT_PNG_LIBRARY:FILEPATH=/usr/lib64/ //Path to a program. QT_QMAKE_EXECUTABLE:FILEPATH=/apps/molekel_related/qt-x11-opensource-src-4.3.0/bin/qmake //Path to a file. 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TK_LIBRARY-ADVANCED:INTERNAL=1 //Modified flag for variable: VTK_DIR VTK_DIR-MODIFIED:INTERNAL=1 //Have library /usr/lib64/;/usr/lib64/ X11_LIB_X11_SOLO:INTERNAL=1 //Advanced flag for variable: X11_X11_INCLUDE_PATH X11_X11_INCLUDE_PATH-ADVANCED:INTERNAL=1 //Advanced flag for variable: X11_X11_LIB X11_X11_LIB-ADVANCED:INTERNAL=1 //Advanced flag for variable: X11_Xext_LIB X11_Xext_LIB-ADVANCED:INTERNAL=1 //Advanced flag for variable: X11_Xlib_INCLUDE_PATH X11_Xlib_INCLUDE_PATH-ADVANCED:INTERNAL=1 //Advanced flag for variable: X11_Xutil_INCLUDE_PATH X11_Xutil_INCLUDE_PATH-ADVANCED:INTERNAL=1
    Re: build error
    Submitted by Molekel Admin; posted on Monday, August 06, 2007
    Hi, the problem is that OpenMOIV was built with fl fonts support. Building OpenMOIV with -Dno_libFL:int=1 should fix the problem. E.g. cmake -Dshared:int=1 -Dno_libFL:int=1 -Dcoin:int=1 -Dsys_fonts:int=1
    Viewing molecular orbitals from Molden files
    Submitted by Molekel Admin; posted on Thursday, August 16, 2007
    Viewing molecular orbitals read from Molden files can be a problem in case the basis set elements are not in the same order as the atoms. This behavior is going to change in the next release of Molekel and a fix has already been committed. In the meantime if you need to visualize molecular orbitals read from Molden you could simply reorder the atoms in the Molden file in the same order as the basis set elements. E.g. In case the atoms are ordered like this: [Atoms] Angs C 1 6 0.0000000000 0.0000000000 0.0000000000 H 2 1 0.0000000000 0.0000000000 1.0856415283 H 3 1 0.0000000000 1.0343722180 -0.3297423077 H 4 1 -0.9307128069 -0.4512369987 -0.3298275233 C 5 6 1.2066572971 -0.7558134495 -0.5524694437 H 6 1 1.2067585831 -1.7901882479 -0.2227929118 H 7 1 2.1373286719 -0.3044302328 -0.2226968903 H 8 1 1.2065923496 -0.7556902812 -1.6381205626 And the basis set is: [GTO] 1 0 ... 5 0 ... 2 0 ... 3 0 ... 4 0 ... 6 0 ... 7 0 ... 8 0 ... If you change to: [Atoms] Angs C 1 6 0.0000000000 0.0000000000 0.0000000000 C 2 6 1.2066572971 -0.7558134495 -0.5524694437 H 3 1 0.0000000000 0.0000000000 1.0856415283 H 4 1 0.0000000000 1.0343722180 -0.3297423077 H 5 1 -0.9307128069 -0.4512369987 -0.3298275233 H 6 1 1.2067585831 -1.7901882479 -0.2227929118 H 7 1 2.1373286719 -0.3044302328 -0.2226968903 H 8 1 1.2065923496 -0.7556902812 -1.6381205626 ... [GTO] 1 0 ... 2 0 ... 3 0 ... 4 0 ... 5 0 ... 6 0 ... 7 0 ... 8 0 ... It should work.
    request for colors and renaming
    Submitted by Benj FitzPatrick; posted on Thursday, August 16, 2007
    I have 2 requests: 1) It would be nice to have an option to change the defaults used by Molekel (colors, bond type, etc). 2) Renaming sub-menus under a molecule would be nice (either by right clicking and getting a menu dropdown or by left clicking twice). I would like this so I could rename orbitals after I generate them so it is easier to keep track of them (C-C sigma means a lot more to me than orbital #3. Thanks, Benj
    Re: request for colors and renaming
    Submitted by Benj FitzPatrick; posted on Saturday, August 18, 2007
    Additionally, it would be nice to have a slider for opacity when transparent solid orbitals are selected.
    Re: request for colors and renaming
    Submitted by Molekel Admin; posted on Friday, August 24, 2007
    Hi, do you want to be able to: [ ] change the default color/transparency for +/- and 0 orbital surfaces; will affect all the orbitals [ ] change the color/transparency on a per-surface basis; will affect only one surface ? Regarding the orbital naming: this is easy to implement so we should be able to add it to the next version of Molekel. Thank you FYI: in the future the "Transparent solid" option will go away, the default will be "Solid" and there will be a transparency slider.
    Re: request for colors and renaming
    Submitted by Benj FitzPatrick; posted on Friday, August 24, 2007
    Good question. Would it be possible to have a checkbox for "use transparency on all orbitals" so that both of the options you listed would be possible? I think this would really only be a minimally harder than the option where each orbital could have individual transparency, right? Thanks.
    Re: request for colors and renaming
    Submitted by Benj FitzPatrick; posted on Friday, August 24, 2007
    As for the color of the orbitals I think that using the same 2 colors for all orbitals should be adequate.
    Frequencies from molden files
    Submitted by John Slattery; posted on Friday, November 09, 2007
    Hi All, When I open a molden input file in molekel (this includes the sample structure included with the package) it does not read the vib. freq. or trajectory parts of the file. I can view the MOs for these structures but not the frequencies or trajectories. Does anyone know what I am doing wrong? Thanks, John
    Re: Frequencies from molden files
    Submitted by Molekel Admin; posted on Thursday, February 14, 2008
    You are not doing anything wrong, it's the Molden reader that is not reading frequency information; this will be fixed by the new OpenBabel Molden reader.
    Viewing e-density surface G03
    Submitted by Tim Cook; posted on Thursday, February 28, 2008
    I can read in a Gaussian 03 .log file to visualize a molecule, but when I try to generate electron density surfaces everything is grayed out as if the log file doesn't contain the necessary information. If I run the same input file in Gaussian 98 the resulting .log file does allow surfaces to be visualized. I've found that I can take the first part of the G98 log file, everything above the pseudo-potentials, and paste it over the corresponding first part of the G03 log file, and then everything works fine. The information I'm copying and pasting is almost identical, it just seems that the basis set is formatted slightly differently in the G03 log, and that throws things off. Also, is there a way to generate more than one surface at one time? The ability to save all orbital pictures with one action is great, but it would be nice to be able to generate them in a similar way. When I select multiple orbitals by holding shift or control, only the last one gets generate upon clicking 'generate'. Lastly, a quick question. Do surfaces need to be generated every time you open the log file again, or is there a way to save surfaces and reload them. In the old version I used .MACU files were generated which could quickly be read back in, but I haven't seen anything like that in the newest version. Thanks for any help in advance!
    Re: Viewing e-density surface G03
    Submitted by Tim Cook; posted on Thursday, February 28, 2008
    P.S. Sorry about posting this here, I didn't see the "help" forum until after I made this post. To keep from cluttering things, I won't repost it there. I saw the bit about changing gfprint to iop(3/24=1) in the help forum for making G03 outputs able to generate surfaces, I'll try that, thanks. I also saw the bit about saving surfaces so you don't have to generate them each time. So I guess the only thing left in my questions would be is there a way to generate a bunch of surfaces at once, rather than one at a time? Thanks
    Re: Viewing e-density surface G03
    Submitted by Molekel Admin; posted on Monday, March 03, 2008
    Hi, there is currently no way of generating multiple surfaces at once, this feature has been available in a couple of development versions and then removed because of some issues with multi-threading (different behavior on different systems). When generating multiple surfaces it might take several minutes for the operation to complete and the user should be able to safely stop processing at any time which is not currently supported. This should change in the next versions when we'll reintroduce support for stopping computation.
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