VMD-L Mailing List

From: James MacDonald (j.macdonald_at_mail.cryst.bbk.ac.uk)
Date: Tue Mar 01 2005 - 17:17:15 CST

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
>