VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 20 2020 - 13:44:01 CST

The symlink is needed so that in larger build environments, like ours,
many different plugin build areas can be used/tested, and it's up to
the person doing the VMD build which built plugin tree they want to include
in the final make_distrib step...

Best,
  John

On Thu, Feb 20, 2020 at 02:32:45PM -0500, Joe Konecny wrote:
> Yeah I ran make distrib. That tree listing was PLUGINDIR which is
> /home/pi/vmd-1.9.4a38/plugins and not the plugin src directory.
> This is what I assume make distrib created. Why is the symlink
> needed? Doesn't make distrib just cp everything?
>
>
> PLUGINDIR=/home/pi/vmd-1.9.4a38/plugins
>
>
>
>
> On 2/20/20 2:24 PM, John Stone wrote:
> >Did you do "make distrib" step to copy the plugins from the compile
> >area into the form used for the VMD installation image? You have to have
> >a PLUGINDIR environment variable set, and normally you'd symlink from
> >that area into vmd/plugins, so that when you do "make_distrib" in the
> >VMD build area, it will pick up the install-ready plugin tree as needed.
> >
> >Best,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Feb 20, 2020 at 02:13:47PM -0500, Joe Konecny wrote:
> >>Can anyone confirm what the plugin directory is supposed to look
> >>like? After an apparently successful compile and install here is what I
> >>see...
> >>
> >>(I've linked it with pastebin because it's a large tree listing)
> >>
> >>In ~/vmd-1.9.4a38/plugins
> >>
> >>
> >>https://pastebin.com/HrmQMTYs
> >>
> >>
> >>
> >>
> >>
> >>
> >>On 2/19/20 2:00 PM, John Stone wrote:
> >>>Hi,
> >>> I've got to run to a meeting, but you're a reasonable fraction of
> >>>the way there. It appears that something went wrong in terms of your
> >>>compilation/installation of the VMD plugins, but otherwise the startup
> >>>messages are fairly reasonable. I don't think a Pi can handle GLSL, so
> >>>that's no surprise.
> >>>
> >>>Best,
> >>> John
> >>>
> >>>On Wed, Feb 19, 2020 at 10:39:31AM -0500, Joe Konecny wrote:
> >>>>I have absolutely zero knowledge on what vmd does but a friend asked
> >>>>me to get it running on raspberry pi. So I did but I noticed a few
> >>>>messages on startup that makes me wonder if it will work correctly
> >>>>for him. Mainly with GLSL rendering and packages that could not be
> >>>>loaded. Can anyone comment on these messages and how they will
> >>>>affect the ability of vmd to do what it's supposed to do?
> >>>>
> >>>>
> >>>>pi_at_raspberrypi:~/vmd-1.9.4a38/LINUXAARCH64ARM $ ./vmd_LINUXAARCH64ARM
> >>>>Info) VMD for LINUXAARCH64ARM, version 1.9.4a38 (February 19, 2020)
> >>>>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: 3695MB (94%)
> >>>>Warning) Detected X11 'Composite' extension: if incorrect display occurs
> >>>>Warning) try disabling this X server option. Most OpenGL drivers
> >>>>Warning) disable stereoscopic display when 'Composite' is enabled.
> >>>>Warning) Simple graphics mode: OpenGL 1.0, no extensions
> >>>>Info) OpenGL renderer: V3D 4.2
> >>>>Info) Features:
> >>>>Info) GLSL rendering mode is NOT available.
> >>>>The irspecgui package could not be loaded:
> >>>>
> >>>>The multiseq package could not be loaded:
> >>>>
> >>>>The networkview package could not be loaded:
> >>>>
> >>>>The pmepot_gui package could not be loaded:
> >>>>
> >>>>The autoionizegui package could not be loaded:
> >>>>
> >>>>The solvate package could not be loaded:
> >>>>
> >>>>The autopsf package could not be loaded:
> >>>>
> >>>>The cggui package could not be loaded:
> >>>>
> >>>>The dowser_gui package could not be loaded:
> >>>>
> >>>>The chirality_gui package could not be loaded:
> >>>>
> >>>>The cispeptide_gui package could not be loaded:
> >>>>
> >>>>The forcefieldtoolkit package could not be loaded:
> >>>>
> >>>>The mdff_gui package could not be loaded:
> >>>>
> >>>>The membrane package could not be loaded:
> >>>>
> >>>>The mergestructs package could not be loaded:
> >>>>
> >>>>The molefacture package could not be loaded:
> >>>>
> >>>>The mutator package could not be loaded:
> >>>>
> >>>>The alascan package could not be loaded:
> >>>>
> >>>>The autoimd package could not be loaded:
> >>>>
> >>>>The qwikmd package could not be loaded:
> >>>>
> >>>>vmd > Info) Using plugin pdb for structure file /home/pi/m.pdb
> >>>>Info) Using plugin pdb for coordinates from file /home/pi/m.pdb
> >>>>Info) Determining bond structure from distance search ...
> >>>>Info) Analyzing structure ...
> >>>>Info) Atoms: 17
> >>>>Info) Bonds: 16
> >>>>Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> >>>>Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> >>>>Info) Residues: 2
> >>>>Info) Waters: 0
> >>>>Info) Segments: 1
> >>>>Info) Fragments: 1 Protein: 1 Nucleic: 0
> >>>>Info) Finished with coordinate file /home/pi/m.pdb.
> >>>>Info) VMD for LINUXAARCH64ARM, version 1.9.4a38 (February 19, 2020)
> >>>>Info) Exiting normally.
> >>>
> > 

-- 
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/