From: nealec (nealec_at_rpi.edu)
Date: Fri Dec 12 2014 - 23:55:20 CST

Dear John:

Your suggestion works great. Thank you so much for your help.

Chris.

On 2014-12-12 21:33, John Stone wrote:
> 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.