VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 09 2008 - 10:52:00 CDT

Hi,
  It sounds to me like your self-compiled VMD installation is missing
the contents of its plugins directory tree. When you compiled your
VMD plugin tree, did you also do a "make distrib" to copy the plugin
tree to the directory used by your VMD compilation? You can check the
contents of the plugin tree in your installed VMD, you should see something
like this:
  % ls /Projects/vmd/pub/linux/lib/vmd187a30/plugins
  include LINUX noarch

  % ls /Projects/vmd/pub/linux/lib/vmd187a30/plugins/noarch/tcl
  apbsrun1.3 extendedpdb1.0 navfly1.0 runante0.1
  atomedit1.0 gofrgui1.0 navigate1.0 saltbr1.0
  autoimd1.6 hbonds1.0 optimization1.0 seqdata1.0
  autoionize1.2 idatm0.1 palettetool1.0 seqedit1.0
  bignum1.0 imdmenu1.0 paratool1.3 simpleedit1.0
  biocore1.1 inorganicbuilder0.1 pbctools2.2 solvate1.2
  blast1.0 membrane1.0 pdbtool1.0 ssrestraints1.0
  cgtools1.0 mergestructs1.0 phylotree1.0 stingtool1.0
  cliptool1.0 molefacture1.1 plotter1.2 textview1.1
  clonerep1.1 moltoptools0.1 qmtool1.1 timeline1.0
  colorbar1.0 multimolanim1.0 ramaplot1.1 utilities1.0
  colorscalebar1.2 multiplot1.1 readcharmmpar1.0 vdna1.2
  contactmap1.1 multiseq2.0 readcharmmtop1.0 viewmaster2.2
  dataimport1.0 multiseqdialog1.0 resptool1.1 vmdmovie1.6
  demomaster1.0 namdenergy1.2 rmsd1.0 vmdtkcon1.0
  dipwatch1.1 namdgui1.1 rmsdtt2.0 volmapgui1.0
  dowser1.0 namdplot1.0 rnaview1.0 zoomseq1.0
  exectool1.2 namdserver1.1 ruler1.0

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 08, 2008 at 04:46:07PM -0700, Janet Jacobsen wrote:
> Hi. I was asked to upgrade VMD from 1.8.3 to 1.8.6 on
> a multi-user system for which I do not have root access.
> It's a Linux x86_64 system (kernel 2.6.5).
>
> I'll skip the details, but I went down the path of building
> fltk, netcdf, the VMD plugins, and VMD with a version of
> gcc that is consistent with the version of GL on the machine.
>
> I cannot run vmd using the vmd script in ~bin (when I load
> a molecule all windows disappear), but with the version I built,
> I am able to run vmd by executing the binary in ~lib/vmd.
>
> I have run through the tutorial and tried loading a few proteins,
> and most of that seems to work, but the Extensions menu is
> blank.
>
> When I fire up VMD 1.8.3, I see a lot of entries in the Extensions
> menu, so I assume that I should see the same extensions when
> I start VMD 1.8.6. Any idea what step I may have missed in
> building VMD? (As I mentioned above, I did compile the VMD
> plugins, and I did define PLUGINDIR before compiling VMD.)
>
> In general, I am confused about the difference between extensions
> and plugins. I tried experimenting with the .vmdrc file and with
> "package require" at the command line, but based on my
> understanding of the plugin documentation, I shouldn't need to
> add plugins that come with the VMD distribution.
>
> I'd appreciate any pointers you can give me.
>
> Thanks,
> Janet 

-- 
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