VMD-L Mailing List

From: James MacDonald (j.macdonald_at_mail.cryst.bbk.ac.uk)
Date: Tue Mar 01 2005 - 17:46:09 CST

Hi John,

I've only recently did a clean install of FC3 on this machine so I don't
have a great deal on it. I don't have a .cshrc file at all because i'm
using bash as the default shell. If i run 'vmd -dispdev text' i get

Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
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, 2 CPUs detected.
vmd >

so it looks fine.

I can also run the /usr/local/lib/vmd/vmd_LINUX binary directly and get
the OpenGL window and load in and display trajectories but obviously the
environmental variables are missing so I get these messages:

Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
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, 2 CPUs detected.
Info) OpenGL renderer: RADEON X300 Generic
Info) Features: STENCIL RN MDE CVA MTX PP PS GLSL(OVF)
ERROR) Unable to locate VMD vertex and fragment shader path, VMDDIR
environment variable not set
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), 3-D (2048x2048x2048), Multitexture
(8)
ERROR) Tcl startup error: Can't find a usable init.tcl in the following
directories:
ERROR) /usr/local/lib/tcl8.4 /usr/local/lib/lib/tcl8.4 /usr/local/lib/tcl8.4 /usr/local/lib/library /usr/local/library /usr/local/tcl8.4.1/library /usr/tcl8.4.1/library /usr/local/lib/tcl8.4
ERROR)
ERROR)
ERROR)
ERROR) This probably means that Tcl wasn't installed properly.
ERROR) Tk startup error: invalid command name "tcl_findLibrary"
ERROR) VMDDIR undefined, startup failure likely.
ERROR) Could not read the vmd initialization file -
ERROR) source {/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl}
ERROR) can't find package http 2.4
ERROR) The VMDDIR environment variable is set by the startup
ERROR) script and should point to the top of the VMD hierarchy.
ERROR) VMD will continue with limited functionality.
ERROR) invalid command name "vmd_load_extension_packages"

thanks,

James.

PS I hope you are well!

On Tue, 2005-03-01 at 17:29 -0600, John Stone wrote:
> James,
> Have you tried renaming your .cshrc file to see if your login scripts
> are the source of the problem? If that didn't cure the problem, then you
> may in fact have a different problem than Daniel did. There are various
> things that can potentially cause this behavior. I assume you're running
> the 32-bit version of VMD right? What happens if you run 'vmd -dispdev text'?
> Does that work? If so, then you have a graphics problem of some sort.
> If not, then it's probably an environment or shared library issue.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, Mar 01, 2005 at 11:17:15PM +0000, James MacDonald wrote:
> >
> > Hi all,
> >
> > Has the problem with installing VMD 1.8.3 on Fedora Core 3 been solved
> > because I'm suffering exactly the same problem as Daniel (main window
> > flashing up and disappearing on startup...) but I don't have InsightII
> > installed? I had a previous installation of VMD 1.8.2 which I deleted
> > and which did work fine.
> >
> > I had a look through the mailing list for a solution to his problem but
> > couldn't find one, so apologies if any one has to repeat themselves!
> >
> >
> > James.
> >
> >
> >
> > On Wed, 2005-01-12 at 09:33 +0200, Dr. Daniel James White PhD wrote:
> > > Hi,
> > >
> > > There seems to be a conflict between InsightII from acellrys,
> > > and VMD
> > >
> > > InsightII requires that the following cshrc file is sourced before
> > > insightII is launched
> > > so I was instructed to put a line in my .cshrc to source this file
> > >
> > > this is what causes vmd to fail
> > > I wouldn't be surprised is there is a problem here as the linux support
> > > for InsightII from accelrys is very new ? it's not even working at the
> > > moment for some odd reason ( although before Xmas it was...... fedora
> > > core 3 self updates likely to be the problem there, but I digress....)
> > >
> > > any clues ?
> > >
> > > Dan
> > >
> > >
> > > # cshrc
> > > # Environment definition script for Accelrys software.
> > > #
> > > # Place the following line in the ~/.cshrc file of any user
> > > # desiring to use Accelrys software products:
> > > #
> > > # source /usr/msi/cshrc
> > > #
> > > # Accelrys Inc. 2001
> > > #---------------------------------------------------------------
> > >
> > > source /home/dan/Desktop/insightII/cdrom/License_Pack/msi_lic_cshrc
> > >
> > > # Set the BIOSYM_ROOT environment variable to point to the root
> > > # of the Installation tree and set BIOSYM_CONTEXT to the default
> > > context.
> > > setenv BIOSYM_ROOT /usr/local/accelrys
> > > if ($?BIOSYM_CONTEXT == 0) setenv BIOSYM_CONTEXT I2000.3
> > >
> > > # Set up additional interactive environment variables.
> > > setenv BIOSYM ${BIOSYM_ROOT}/${BIOSYM_CONTEXT}
> > > setenv BIOSYM `echo $BIOSYM | sed 's%//%/%g' `
> > > #source $BIOSYM/config/special/cshrc_platform # Set BIOSYM_PLATFORM
> > >
> > > # Create set_biosym_context alias
> > > alias set_biosym_context \
> > > 'setenv setcontext_arg "\!:*"; source $BIOSYM_ROOT/biosym_setcon'
> > >
> > > # Create set_context alias
> > > alias set_context \
> > > 'setenv setcontext_arg "\!:*"; source $BIOSYM_ROOT/biosym_setcon'
> > >
> > > alias reset_env \
> > > 'setenv setcontext_arg $BIOSYM_CONTEXT; unsetenv BIOSYM_CONTEXT;
> > > source $BIOSYM_ROOT/biosym_setcon'
> > >
> > > # Use biosym_setcon to define context
> > > setenv setcontext_arg $BIOSYM_CONTEXT
> > > setenv BIOSYM_CONTEXT Undefined
> > > source $BIOSYM_ROOT/biosym_setcon
> > >
> > >
> > > On 11 Jan 2005, at 18:50, Axel Kohlmeyer wrote:
> > >
> > > >
> > > >>>> "DW" == Daniel James White PhD <Dr.> writes:
> > > >
> > > >
> > > > dan,
> > > >
> > > > this check is easy. just rename your .cshrc to .disabled.cshrc
> > > > or something else and try again. for some setups you have to
> > > > log out and back in to have this change take full effect.
> > > >
> > > > axel.
> > > >
> > > >
> > > > DW> Hi John,
> > > >
> > > > DW> I have stuff added to my .cshrc file for insightII
> > > >
> > > > DW> I can start csh and tcsh
> > > > DW> with no errors output to the terminal....
> > > >
> > > > DW> so how do I check if something really is bombing but the shell isnt
> > > > DW> telling me?
> > > >
> > > > DW> Dan
> > > >
> > > >
> > > > [...]
> > > >
> > > >
> > > >
> > > > --
> > > >
> > > > =======================================================================
> > > > Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> > > > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> > > > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> > > > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> > > > =======================================================================
> > > > If you make something idiot-proof, the universe creates a better idiot.
> > > >
> > > >
> > > Dr. Daniel James White BSc. (Hons.) PhD
> > > Bioimaging Coordinator
> > > Nanoscience Centre and
> > > Department of Biological and Environmental science
> > > Division of Molecular Recognition
> > > Ambiotica C242
> > > PO Box 35
> > > University of Jyväskylä
> > > Jyväskylä FIN 40014
> > > Finland
> > > +358 14 260 4183 (work)
> > > +358 468102840 (mobile)
> > >
> > > http://www.chalkie.org.uk
> > > dan_at_chalkie.org.uk
> > > white_at_cc.jyu.fi
> > >
>