From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Sat May 12 2007 - 19:31:09 CDT

Hi Guys,

I don't know if this appropriate for the VMD list but..

Does anyone know if it is possible to perform VMD-style manipulations
in JMV? I would be particularly interested in rotating part of a
molecule, while keeping the remainder unmoved. Is JMV just a viewer,
like jmol, or does it have additional structural processing
capabilities such as these?

Sam

On May 1, 2007, at 3:29 PM, Jan Rychter wrote:

>> Jan,
>> The reason your build used X11 rather than Aqua was because
>> it was compiled with "OPENGL" rather than "FLTKOPENGL". We normally
>> compile the MacOS X Intel version of VMD with:
>> MACOSXX86 FLTKOPENGL FLTK IMD TK TCL SILENT SPACEBALL PTHREADS
>> LIBTACHYON \
>> ACTC NETCDF
>
> Thanks -- that's a good hint!
>
>> I don't know what makefile editing you did, but I suspect it was
>> due to the use of non-framework versions of Tcl/Tck/etc. If you
>> tell me
>> more specifically what you're doing, I should be able to help you get
>> things working.
>
> Ok, so here is where I am right now.
>
> I use the following flag set: MACOSXX86 FLTKOPENGL FLTK TK TCL
> PYTHON PTHREADS NUMPY
>
> I made the following modifications to configure:
> ----------------------------------------------------------------------
> ----------------------------
> diff -u ../original/vmd-1.8.6/configure configure
> --- ../original/vmd-1.8.6/configure 2007-04-08
> 07:03:49.000000000 +0200
> +++ configure 2007-05-01 21:22:36.000000000 +0200
> @@ -1814,7 +1814,7 @@
> # Set Python paths to use the system-provided Python rather than
> # our own, since Apple MacOS X 10.4.x or newer includes Python
> 2.3
> # by default.
> - $python_include = "-F/System/Library/Frameworks";
> + $python_include = "-I/Library/Frameworks/Python.framework/
> Versions/2.5/lib/python2.5/site-packages/numpy/core/include -F/
> Library/Frameworks -F/System/Library/Frameworks";
> $python_library = "";
> $python_libs = "-framework Python -lpthread";
>
> @@ -1851,8 +1851,8 @@
> ## MacOS X native builds using Tcl/Tck frameworks
> ##
> ## use the Tcl/Tk frameworks provided by apple, when we use
> their Python
> -# $tcl_include = "-F/System/Library/Frameworks";
> -# $tcl_library = "-F/System/Library/Frameworks";
> + $tcl_include = "-F/Library/Frameworks";
> + $tcl_library = "-F/Library/Frameworks";
>
> ## use our own Tcl/Tk framework builds when not compiling
> with Python,
> ## as Apple's currently shipping versions are quite buggy
> @@ -1895,9 +1895,9 @@
> $def_imageviewer="/usr/bin/open %s";
>
> # Hack the FLTK paths to use 1.1.7 rather than 1.1.4
> - $fltk_include = "-I$fltk_dir/fltk-1.1.7";
> - $fltk_library = "-L$fltk_dir/$config_arch";
> - $fltk_libs = "-lfltk -lX11";
> + $fltk_include = "-I/opt/local/include";
> + $fltk_library = "-L/opt/local/lib";
> + $fltk_libs = "-lfltk";
>
> # Set Python paths to use the system-provided Python rather than
> # our own, since Apple MacOS X 10.4.x or newer includes Python
> 2.3
> @@ -1956,8 +1956,8 @@
> $tcl_libs = "-framework Tcl";
> if ($config_tk) { $tcl_libs = "-framework Tk " . $tcl_libs; }
>
> - $vmd_include = "$tcl_include";
> - $vmd_library = "$tcl_library";
> + $vmd_include = "-F/Library/Frameworks -I/Library/
> Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-
> packages/numpy/core/include $tcl_include";
> + $vmd_library = "-F/Library/Frameworks $tcl_library";
> $vmd_libs = "$tcl_libs";
>
> # MacOS 10.3 stuff
> ----------------------------------------------------------------------
> ----------------------------
>
> ... and now the compilation bombs out like this:
>
> c++ -fPIC -Os -ffast-math -DARCH_MACOSXX86 -DVMDOPENGL -
> DVMDFLTKOPENGL -DVMDGRAPHICS -DVMDPYTHON -DVMDTHREADS -
> DUSEPOSIXTHREADS -D_REENTRANT -DVMDNUMPY -DVMDSURF -DVMDMSMS -
> DVMDFIELDLINES -DVMDVOLUMETEXTURE -DVMDTCL -DVMDTK -
> DVMDSTATICPLUGINS -DVMDGUI -DVMDFLTK -F/System/Library/
> Frameworks -F/Library/Frameworks -I/Library/Frameworks/
> Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/
> core/include -I../lib/tcl/include -I../lib/tk/lib_MACOSXX86/
> Tk.framework/Versions/8.4/Headers -I../plugins/include -I../plugins/
> MACOSXX86/molfile -I/opt/local/include -I. -I../src -o
> vmd_MACOSXX86 FltkOpenGLDisplayDevice.o OpenGLExtensions.o
> OpenGLRenderer.o OpenGLShader.o OpenGLCache.o Hershey.o
> PythonTextInterp.o VMDTkinterMenu.o py_animate.o py_atomsel.o
> py_atomselection.o py_axes.o py_color.o py_commands.o py_display.o
> py_graphics.o py_imd.o py_label.o py_material.o py_menu.o
> py_molecule.o py_molrep.o py_mouse.o py_render.o py_trans.o
> py_numeric.o Animation.o ArtDisplayDevic!
> e.o AtomColor.o AtomParser.o AtomLexer.o AtomRep.o AtomSel.o
> Axes.o BaseMolecule.o BondSearch.o CmdAnimate.o CmdColor.o
> CmdDisplay.o CmdLabel.o CmdMaterial.o CmdMenu.o CmdMol.o
> CmdRender.o CmdTrans.o CommandQueue.o CoorPluginData.o CUDAAccel.o
> DisplayDevice.o Displayable.o DisplayRocker.o DispCmds.o
> DrawMolecule.o DrawMolItem.o DrawMolItem2.o DrawMolItemRibbons.o
> DrawMolItemMSMS.o DrawMolItemRings.o DrawMolItemSurface.o
> DrawMolItemVolume.o DrawForce.o DrawRingsUtils.o FileRenderList.o
> FileRenderer.o FPS.o GelatoDisplayDevice.o GeometryAngle.o
> GeometryAtom.o GeometryBond.o GeometryDihedral.o GeometryList.o
> GeometryMol.o GeometrySpring.o Inform.o ImageIO.o Isosurface.o
> JRegex.o JString.o macosxvmdstart.o MaterialList.o Matrix4.o
> Measure.o Molecule.o MoleculeList.o MoleculeGraphics.o
> MolFilePlugin.o Mouse.o MSMSInterface.o PeriodicTable.o
> P_JoystickTool.o P_TugTool.o P_GrabTool.o P_PrintTool.o
> P_PinchTool.o P_UIVR.o P_Buttons.o P_Tracker.o P_Tool.o P_CmdTool.o
> P_SensorConfig.o!
> ParseTree.o PickList.o PickModeAddBond.o PickModeCenter.o Pic!
> kModeFor
> ce.o PickModeList.o PickModeMolLabel.o PickModeMove.o
> PickModeUser.o PlainTextInterp.o PluginMgr.o POV3DisplayDevice.o
> PSDisplayDevice.o VMDQuat.o RadianceDisplayDevice.o
> RayShadeDisplayDevice.o R3dDisplayDevice.o RenderManDisplayDevice.o
> Scene.o SnapshotDisplayDevice.o SpringTool.o Stage.o
> STLDisplayDevice.o Stride.o Surf.o SymbolTable.o
> TachyonDisplayDevice.o Timestep.o UIObject.o UIText.o VMDApp.o
> VMDCollab.o VMDDir.o VMDDisplayList.o VMDMenu.o VMDTitle.o
> VMDThreads.o VolCPotential.o VolMap.o VolMapCreate.o
> VolumetricData.o VolumeTexture.o VrmlDisplayDevice.o
> Vrml2DisplayDevice.o WavefrontDisplayDevice.o utilities.o vmd.o
> vmdmain.o ColorInfo.o TclCommands.o TclMeasure.o TclMolInfo.o
> TclTextInterp.o TclVec.o TclGraphics.o TclVolMap.o cmd_animate.o
> cmd_collab.o cmd_color.o cmd_display.o cmd_imd.o cmd_label.o
> cmd_material.o cmd_menu.o cmd_mol.o cmd_mouse.o cmd_plugin.o
> cmd_render.o cmd_tool.o cmd_trans.o cmd_user.o cmd_util.o
> tcl_commands.o VMDTkMenu.o ColorFltkMenu.o Displa!
> yFltkMenu.o FileChooserFltkMenu.o GraphicsFltkMenu.o
> SelectionBuilder.o GeometryFltkMenu.o MaterialFltkMenu.o
> MolBrowser.o RenderFltkMenu.o SaveTrajectoryFltkMenu.o
> VMDFltkMenu.o MainFltkMenu.o ToolFltkMenu.o frame_selector.o hash.o
> inthash.o intstack.o vmdsock.o vmddlopen.o pcre.o fitrms.o -F/
> Library/Frameworks -F../lib/tcl/lib_MACOSXX86 -F../lib/tk/
> lib_MACOSXX86 -Wl,-executable_path . -lmx -L../plugins/MACOSXX86/
> molfile -L/opt/local/lib -framework OpenGL -framework AGL -
> framework Python -lpthread -lpthread -framework Tk -framework Tcl -
> lmolfile_plugin -lfltk_gl -lfltk -framework Carbon ;
> Linking vmd_MACOSXX86 ...
> /usr/bin/ld: warning -F: directory name (../lib/tcl/lib_MACOSXX86)
> does not exist
> /usr/bin/ld: warning -F: directory name (../lib/tk/lib_MACOSXX86)
> does not exist
> /Developer/Tools/Rez -t APPL -o ../MACOSXX86/vmd_MACOSXX86 vmdmac.r
> ### /Developer/Tools/Rez - SysError 0 during open of "vmdmac.r".
> Fatal Error!
> ### /Developer/Tools/Rez - Fatal Error, can't recover.
> vmdmac.r: ### /Developer/Tools/Rez - Since errors occurred, ../
> MACOSXX86/vmd_MACOSXX86's resource fork was not written.
> make: *** [vmd_MACOSXX86] Error 3
>
> Any help is very much appreciated.
>
> --J.
>
>> On Mon, Apr 30, 2007 at 12:39:33PM +0200, Jan Rychter wrote:
>>> Hi,
>>>
>>> Does anyone have a build of VMD running under Mac OS X (Intel) with
>>> Python support?
>>>
>>> I've been trying to compile vmd 1.8.6 on MacOS X (10.4.9, Intel)
>>> with
>>> Python support (I have 2.5 installed), and gave up. After much, much
>>> fighting and manual makefile editing I got the executable to
>>> actually
>>> build and link, but now running it results in a segfault. The
>>> terminal
>>> says:
>>>
>>> [12:35] tnuctip:/Users/jwr>/Applications/VMD\ 1.8.6\ jwr.app/
>>> Contents/MacOS/startup.command; exit
>>> Info) VMD for MACOSXX86, version 1.8.6 (April 29, 2007)
>>> [...]
>>> Info) Multithreading available, 2 CPUs detected.
>>> ERROR) Exiting due to X-Windows OpenGL window creation failure.
>>> Info) VMD for MACOSXX86, version 1.8.6 (April 29, 2007)
>>> Info) Unable to create OpenGL window.
>>>
>>> I have no idea why it tries to use X11, I thought it would use
>>> native
>>> GL. I have it configured with
>>> MACOSXX86 OPENGL TK TCL PYTHON PTHREADS NUMPY
>>>
>>> Any ideas? Perhaps someone has built such a binary and would be kind
>>> enough to provide it?
>>>
>>> --J.