From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 12 2014 - 20:33:04 CST

Hi,
  In general, when using plugins via scripts, it is correct practice
to use the Tcl "package require" commands to cause them to be loaded.
When you run VMD in graphical mode, some of the plugins get loaded
by virtue of being added to the VMD extensions menu, but as you have
discovered, this is not the case when running in text mode. The correct
way to refer to any plugin is to use "package require XXX" where XXX is
replaced by the name of the plugin you want to use.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 12, 2014 at 09:17:09PM -0500, nealec wrote:
> Dear users:
>
> I would like to use the chirality and cispeptide plugins to vmd in text
> mode. However, I am having difficulty.
>
> Everything works fine if I open it with the visualization and then, in
> the tkconsole window:
>
> loading history file ... 13 events added
> Main console display active (Tcl8.5.6 / Tk8.5.6)
> (GET_STRUCT) 14 % chirality
> Usage: chirality <command> [args...]
> Commands:
> check -- identify chirality errors
> list -- list identified chirality errors
> minimize -- fix chirality errors using energy minimization
> move -- move hydrogen atom to fix chirality
> reset -- reinitialize plugin state
> restrain -- generate NAMD extrabonds file to prevent chirality changes
> show -- visualize identified chirality errors
>
> >Main< (GET_STRUCT) 15 % cispeptide
> Usage: cispeptide <command> [args...]
> Commands:
> check -- identify cis peptide bonds
> list -- list identified cis peptide bonds
> minimize -- fix cis peptide bonds using energy minimization
> move -- move specified atom to convert to trans
> reset -- reinitialize plugin state
> restrain -- generate NAMD extrabonds file to restrain peptide bonds
> set -- define how to modify a given cis peptide bond
> show -- visualize identified cis peptide bonds
>
> ##############
>
> However, when I try from the command line on the same computer:
>
> [nealec_at_pegasus GET_STRUCT]$ vmd -dispdev text
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) Free system memory: 1489MB (37%)
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> Info) No CUDA accelerator devices available.
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/vmd/lib/plugins/LINUXAMD64/molfile
> /home/nealec/exe/BENDIX /usr/local/vmd/lib/scripts/tcl8.5
> /usr/local/vmd/lib/scripts /usr/local/vmd/lib
> /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/vmd/lib/scripts/vmd /usr/local/vmd/lib/plugins/LINUXAMD64/tcl
> /usr/local/vmd/lib/plugins/noarch/tcl
> The bendix package could not be loaded:
>
> vmd > chirality
> invalid command name "chirality"
> vmd > cispeptide
> invalid command name "cispeptide"
> vmd >
>
>
> Is there any way to get these two plugins to work from the command line
> (i.e., on a cluster)? Note that I also tried "vmd -dispdev win" on a
> cluster, got the same access to the command line, and again these
> plugins were not usable.
>
> Thank you for your help,
> Chris.

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