From: John Stone (
Date: Thu Oct 23 2014 - 15:43:35 CDT

  If the extensions menu is empty, I would guess that either the
VMD plugins didn't get installed correctly, or there's something
amiss with their dependencies. Normally VMD would complain vociferously
during startup if there's something wrong here. Do you get a couple
of pages of warnings about plugins not being able to load correctly
during VMD startup?

  John Stone

On Thu, Oct 23, 2014 at 06:15:05PM +0000, 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.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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