VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 14 2007 - 12:51:15 CDT

Hi Sam,
  No JMV, can't do things like that. It was intended merely as
a viewing tool, and thus it doesn't have those capabilities.
We had pursued developing it while Java3D was doing well and was
easily integrated with web browsers, before tools like JMol were
around. Since then, Java3D languished significantly, and the use of
Java3D began requiring the installation of various java plugins
and performing various complex setup tasks for each web browser
which ultimately made it much less interesting to us since the performance
of Java graphics is tremendously limited without the use of something
like Java3D or one of the OpenGL bindings for Java, which would prevent
us from doing the kinds of visualizations we like to do in VMD.
Overall, it now appears that we may be better off pursuing the use
of 3-D models (Adobe Acrobat3D) with complex hierarchies of geometry
to emulate what we can do in a real molecular visualization program
like VMD. Acrobat3D is already more widespread than Java3D was
(it works on all of the platforms supported by Acrobat Reader already)
when we wrote JMV. We're currently looking at doing more with
Acrobat3D rather than developing JMV further, particularly since it
gives us a better method of doing electronic textbooks than was possible
even using JMV.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 12, 2007 at 08:31:09PM -0400, Samuel Flores wrote:
> 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. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078