From: Josh Vermaas (
Date: Thu Oct 23 2014 - 14:14:12 CDT

Hmm... John would know more about if the leftovers can cause problems.
To check, I'd change the config and makefiles so that it will install to
a different location (your home directory?), and then run VMD directly
from this new install location rather than the one in /usr/local as a
test. I've never personally seen this behavior, and don't know the
details of how the extensions tree is populated, so I'm afraid I can't
be more helpful.
On 10/23/2014 01:15 PM, Woodson, Michael wrote:
> Hi Josh, I am not using a script to compile and install vmd. I was not
> using any options for configuring the plugins directory, or for make
> distrib. I tried mimicking the options in your script, but I still
> have the same problem.
> In the past, I had strange problems when past versions hadn't been
> uninstalled completely, so I wonder if there might be a problem with
> previous installations, but I don't know what to do other than delete
> the /usr/local/lib/vmd directory and /usr/local/bin/vmd
> ------------------------------------------------------------------------
> *From:* Josh Vermaas []
> *Sent:* Thursday, October 23, 2014 12:13 PM
> *To:* Woodson, Michael;
> *Subject:* Re: vmd-l: Extensions menu empty
> Hi Mike,
> What were your configure options or the options for make distrib? My
> understanding is that the extensions menu items are a compile-time
> feature, and if they weren't in place properly during compilation, the
> VMD build will happily (try to) work without any extensions. Your
> .vmdrc lines may ameliorate the situation somewhat (possibly, I've
> never tested this) by providing the facilities so the commands in the
> terminal, but it won't change the extensions menu in my experience.
> This is not the optimal setup, and if I had to make an educated guess,
> make distrib didn't put the plugins where the main program expects
> them, but this normally causes the compilation to halt on missing
> molfiles, so I'm not sure what the issue is specifically. This is my
> compile and install makefile (adapted for not making debian packages)
> that is placed in the directory *above* the plugins and the source vmd
> directory during compilation. See if this helps at all to sort out
> what might be missing:
> DESTDIR=$(shell pwd)
> VMDVER="1.9.2beta1"
> #These are the final install locations
> PLUGINDIR=/usr/local/lib/vmd/plugins
> PLUGINBINDIR=/usr/local/bin
> export
> all: compileplugins compilevmd
> compileplugins:
> cd plugins; make LINUXAMD64 TCLINC=-I/usr/include/tcl8.6
> TCLLIB=-L/usr/lib \
> NETCDFLIB=-L/usr/lib NETCDFINC=-I/usr/include/ -j 1 ; make distrib
> PLUGINDIR=$(DESTDIR)/vmd-$(VMDVER)/plugins
> compilevmd:
> cd vmd-$(VMDVER); \
> cd src ; make
> installplugins:
> cd plugins ; make distrib
> installvmd:
> cd src; make install
> install: installplugins installvmd
> Now I also needed to make changes within the configure script so VMD
> would pick up my system python libraries (and CUDA, and Optix, and
> pretty much all of the other libraries), but I think you have already
> done this for your own system.
> Good luck!
> -Josh Vermaas
> On 10/23/2014 10:27 AM, Woodson, Michael wrote:
>> Hi, I had written in a few days ago about compiling VMD against my
>> native python build.
>> I thought I had gotten it to work, but I didn't check everything, and
>> now notice that the "Extensions" drop-down menu in the "VMD Main"
>> window isn't populated; clicking on it just brings down a small empty
>> frame.
>> I have these lines:
>> set auto_path [linsert $auto_path 0 [file join $env(HOME) vmdplugins]]
>> and
>> vmd_plugin_scandirectory [file join $env(HOME) vmdplugins [vmdinfo
>> arch] molfile] *.so
>> in my .vmdrc file, and it looks like it is, indeed, executing those
>> commands. The ~/vmdplugins/LINUXAMD64/molfile directory has plenty of
>> * files. So does the directory in the vmd installation
>> directory.
>> The other menus are fine, just Extensions.
>> Any help figuring this out would be greatly appreciated!
>> Mike W.