VMD-L Mailing List

From: kskeby (kks_at_chem.au.dk)
Date: Wed Nov 18 2015 - 10:43:22 CST

Hi Josh

Thanks for the response.

If I open VMD from the command-line as you suggested I get the following errors:
ERROR) Could not read the vmd initialization file -
ERROR) source {/Applications/vmd/vmd-1.9.2/MACOSXX86_64/scripts/vmd/vmdinit.tcl}
ERROR) couldn't read file "/Applications/vmd/vmd-1.9.2/MACOSXX86_64/scripts/vmd/vmdinit.tcl": no such file or directory
ERROR) The VMDDIR environment variable is set by the startup
ERROR) script and should point to the top of the VMD hierarchy.
ERROR) VMD will continue with limited functionality.
ERROR) Color definitions file '/Applications/vmd/vmd-1.9.2/MACOSXX86_64/scripts/vmd/colordefs.dat' does not exist.
ERROR) Parsing color definitions failed.
ERROR) Material definitions file '/Applications/vmd/vmd-1.9.2/MACOSXX86_64/scripts/vmd/materials.dat' does not exist.
ERROR) Parsing material definitions failed.
ERROR) Residue types file '/Applications/vmd/vmd-1.9.2/MACOSXX86_64/scripts/vmd/restypes.dat' does not exist.
ERROR) Parsing residue types failed.
ERROR) Atomselection macro file '/Applications/vmd/vmd-1.9.2/MACOSXX86_64/scripts/vmd/atomselmacros.dat' does not exist.
ERROR) Parsing atomselection macros failed.
FLTK
invalid command name "menu"
invalid command name "menu"
invalid command name "menu"
invalid command name "menu"
vmd > invalid command name "menu"
Unable to change color name
Unable to change color name
Unable to change color name
ERROR) invalid command name "vmd_load_extension_packages"

However, if I create a link like this:
cd /Applications/vmd/vmd-1.9.2
ln -s MACOSXX86_64/vmd_MACOSXX86_64 vmd_MACOSXX86_64

And open vmd using the link, there are no errors, but VMD behaves as before not displaying the loaded molecules.

The FLTK environment variable worked, and the right filebrowser is now shown. Using only scripts is not ideal, but I can definitely live with that. However, problem 3 is still there, no molecule is shown in the display window. Anyone else have any ideas?

Thanks,
Katrine

> On 18 Nov 2015, at 10:45, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
>
> Hi Katrine,
>
> In my limited experience compiling for Mac, everything goes wrong all the time, and I run back to my linux box for all of its python-infused goodies. That being said, it looks like you've gotten reasonably far. What happens if you try to run VMD from the command line? Say: ./MACOSXX86_64/vmd_MACOSXX86_64 -dispdev text? Or better yet: ./MACOSXX86_64/vmd_MACOSXX86_64 -dispdev text -python
>
> When I do that, VMD complains about certain environment variables not being set, but will otherwise behave more or less normally. With regard to your specific questions:
>
> 1.) This might be the evil filechooser problem. John has addressed this in past posts, and while it was originally a Yosemite problem, I don't think El Capitan did anything to solve it. Quoting John:
> "
> The solution is to set an environment variable to tell VMD not to
> use the MacOS-provided file browser window, and to instead use the
> FLTK-based file chooser. This is done by setting the environment variable
> "VMDFILECHOOSER" to the value "FLTK". This can be done in VMD itself
> in the text console, in the user's .vmdrc file, in the global .vmdrc
> file in the VMD.app bundle, or by setting the environment variable in the
> user's Unix shell .bashrc, etc.
>
> To set the variable in VMD or .vmdrc etc, run this command:
> set env(VMDFILECHOOSER) FLTK
>
> To set the variable in bash, add this to .bashrc etc:
> VMDFILECHOOSER=FLTK
> export VMDFILECHOOSER
>
> After the environment variable is set, VMD will use the alternative
> file selector window in the graphical interface, and this should prevent
> the problems you've been encountering.
>
> "
>
> 2.) I think this is why there aren't any official VMD64 bit builds for Mac. Something about FLTK not playing nice. An intermediate workaround might be to load from a script passed along to -e. Its not ideal, but it would work, and more importantly, can now be a python script because you baked in python support! The three line version would be this:
>
> from Molecule import *
> mol=Molecule()
> mol.load("filenamegoeshere")
>
> 3.) Ick. I think it might be related to 1, but I'm not familiar enough with compiling for Mac to know the best way of getting around it. :(
>
> Good luck!
> -Josh Vermaas
>
> On 11/18/2015 08:29 AM, kskeby wrote:
>> Hi
>>
>> I have been trying to compile VMD 1.9.2 with python on my mac running OSX El Capitan (10.11.1). I have managed to make a build, but VMD is not behaving as it should.
>> 1. When I open the molecule file browser and go to browse for a file, I am not able to actually select a file, they are inactive.
>> 2. I can load files using the tk console, but the console is not behaving properly. It seems like it does not alway register when a key is pressed, and when I type letters too fast it does not catch all the letters.
>> 3. When I load a pdf-file and dcd on top of that, no molecule is shown in the OpenGL display.
>>
>> Here are the steps I took to build the binaries:
>>
>> 1. Install fltk
>> I tried doing this with Homebrew, however that does not work with El Capitan, and I eventually found this post (https://github.com/mikepurvis/ros-install-osx/issues/12 <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_mikepurvis_ros-2Dinstall-2Dosx_issues_12&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=oynDKUVxrRrPOCCGdUsp-1XfFUeveRVTboIc3TjshT8&e=>) that said that you can use the following to install fltk:
>> > brew reinstall --devel https://raw.githubusercontent.com/dpo/homebrew/ec46018128dde5bf466b013a6c7086d0880930a3/Library/Formula/fltk.rb <https://urldefense.proofpoint.com/v2/url?u=https-3A__raw.githubusercontent.com_dpo_homebrew_ec46018128dde5bf466b013a6c7086d0880930a3_Library_Formula_fltk.rb&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=rslGEKdfoL3PI3dyCHLKJY55A04b-4Yz8LAjrHzxX_I&e=>
>>
>> 3. I already had Xcode (7.1.1 7B1005) and Command line tools installed, so no need to install Tcl, Tk and OpenGL.
>> I am running Tcl8.5, Tk8.5 and Python2.7.
>>
>> 4. I also had XQuartz (X11, <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.xquartz.org_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=qFtc9v6nVMPt0YDROcyBF2ExWY_93ug0Kv3KY5vhR4U&e=>http://www.xquartz.org/ <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.xquartz.org_&d=BQMDaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=pwKxBcH8lMqXKaUoT-mFtw&m=GtB9mAIZP8Lj0deuq-J8r5-N7obj1HtxIhIx5Mi9lvs&s=mXKoFDV-gkWi-lbNnjyO3mrYSNDqyI3YPMEnxdE_VrQ&e=>) installed, which should also be done manually, because it is not included with OS X anymore (https://support.apple.com/en-us/HT201341 <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.apple.com_en-2Dus_HT201341&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=_6phZeaNsP0OFWQMvNKDEPKqy5pUyUJ6sBJDMBNyDzY&e=>).
>>
>> 5. Extract the VMD tarball
>> > cd /Applications/vmd
>> > tar xvfz vmd-1.9.2.src.tar.gz
>>
>> 6. Compile plugins
>> > cd /Applications/vmd/vmd-1.9.2
>> > mv ../plugins .
>> > cd plugins
>> > export TCLINC=-I/usr/local/include
>> > export TCLLIB=-L/usr/local/lib
>> > make MACOSXX86_64 TCLINC=$TCLINC TCLLIB=$TCLLIB
>>
>> > export PLUGINDIR=/Applications/vmd/vmd-1.9.2/plugins
>>
>> I commented out the following lines in the Makefile:
>> #-mkdir -p $(PLUGINDIR)/include
>> #for header in $(PLUGINHEADERS); do cp -p $(INCLUDEDIR)/$$header $(PLUGINDIR)/include || exit 1 ; done
>> Because I was getting the following error when I tried to do make distrib:
>> Populating distribution directory with compiled plugins
>> cp: /Applications/vmd/plugins/include/vmdplugin.h and include/vmdplugin.h are identical (not copied).
>> make: *** [distrib] Error 1
>>
>> > make distrib
>>
>> 7. Compile VMD
>> > cd /Applications/vmd/vmd-1.9.2/
>>
>> Changed the configure.options file so that it only contained:
>> MACOSXX86_64 FLTKOPENGL FLTK TK TCL PYTHON PTHREADS LP64
>>
>> > ./configure
>> > cd src
>>
>> This is where I really ran into problems. I had a lot of error when I typed make depend, so I have to change the INCDIRS, LIBS, and LIBDIRS in the Makefile. This is what I ended up with which didn’t give me any error in the dependencies:
>> INCDIRS = -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/System/Library/Frameworks -I../plugins/include -I../plugins/MACOSXX86_64/molfile -I. -I/usr/local/include -I/usr/X11/include -I/usr/local/Cellar/fltk/1.3.3-r10866_1/include
>>
>> LIBS = -lfltk_gl -lfltk -framework ApplicationServices -ldl -framework OpenGL -framework AGL -framework Cocoa -framework Python -lpthread -framework Tk -framework Tcl -lmolfile_plugin -framework Carbon $(VMDEXTRALIBS)
>>
>> LIBDIRS = -Wl,-executable_path . -lmx -L../plugins/MACOSXX86_64/molfile -L/usr/local/lib -L/usr/local/Cellar/fltk/1.3.3-r10866_1/lib
>>
>> > make
>> I get this error at the end of the make call:
>> Linking vmd_MACOSXX86_64 ...
>> /Developer/Tools/Rez -t APPL -o ./MACOSXX86_64/vmd_MACOSXX86_64 vmdmac.r
>> make: /Developer/Tools/Rez: No such file or directory
>> make: *** [vmd_MACOSXX86_64] Error 1
>>
>> > make install
>>
>> Even though there was an error when running the make command, the make install command is able to run, and executable files are created in /usr/local/lib/vmd.
>>
>> 8. In order to open VMD I had to create a symbolic link to /usr/local/Cellar/fltk/1.3.3-r10866_1 in /usr/local/opt
>> > cd /usr/local/opt
>> > ln -s /usr/local/Cellar/fltk/1.3.3-r10866_1 fltk
>>
>> I tried attaching some files with the output from the different commands, but my email seemed not to make it on to the mailing list.
>>
>> Is there anyone who can help me figure out what is going on? I would really appreciate it. And please let me know if there is any additional information that you need.
>>
>> Thanks,
>> Katrine
>>
>