VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 08 2007 - 14:20:52 CDT

Hmm,
  Try naming the file .login. Worst case you may need to logout
and log back in in order for MacOS X to pick up the variable.
It has been so long since I did this on bash I don't recall
precisely what I needed to do anymore. Of course, the best solution
would be for the TSRI folks to provide a MacOS X Intel binary, rather
than running their PowerPC version in emulation mode which as you can
guess is also slower than one would like.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 08, 2007 at 01:15:54PM -0600, Ralph Jimenez wrote:
> John,
> As you suggested, I created the .bashrc file in my home directory,
> then started VMD, then ran the puts "$env(VMDMSMSUSEFILE)" command, but
> VMD doesn't see the environment variable. It says:
> can't read "env(VMDMSMSUSEFILE)": no such variable
>
> Thanks,
> Ralph
>
>
> John Stone wrote:
> >Ralph,
> > I don't have a mac in front of me just now, but yes, just try
> >creating a .bashrc file in your home directory consisting of those
> >two commands.
> >You can determine whether VMD is seeing the environment variable
> >by running this command in the VMD text console:
> > puts "$env(VMDMSMSUSEFILE)"
> >
> >>From there, try starting VMD and using MSMS once the variable is
> >set correctly.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Tue, May 08, 2007 at 11:12:33AM -0600, Ralph Jimenez wrote:
> >>John,
> >> Thanks. However, I opened a terminal window and looked in my home
> >>directory (ls -l .*) and did not find a .bashrc or .profile file. My
> >>login shell is set to bash. Where should the .bashrc file be located,
> >>and if I don't find one, should I just create it, with those two
> >>commands you mentioned?
> >> Ralph
> >>
> >>
> >>
> >>John Stone wrote:
> >>>Hi,
> >>> If your login shell on OSX is set to bash, then you'd add these commands
> >>>to your .bashrc or .profile file:
> >>>VMDMSMSUSEFILE=1
> >>>export VMDMSMSUSEFILE
> >>>
> >>>If you're using csh, then you'd add these to .cshrc:
> >>>setenv VMDMSMSUSEFILE 1
> >>>
> >>>Cheers,
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>On Mon, May 07, 2007 at 08:37:38PM -0600, Ralph Jimenez wrote:
> >>>>Dear VMDers:
> >>>>
> >>>>I downloaded MSMS from TSRI's web site, but it doesn't work, probably
> >>>>because my environment variables aren't set. I get the "Could not
> >>>>connect to MSMS server..." error message.
> >>>>
> >>>>I need help with two things, which are alluded to in several places in
> >>>>the VMD docs and mailing list, but I need more explicit instructions:
> >>>>
> >>>>1. Could someone please tell me which commands need to be added to
> >>>>which file so that VMD finds msms?
> >>>>
> >>>>2. The 1.8.6 release notes say "it is necessary to set the
> >>>>VMDMSMSUSEFILE environment variable to work around incompatible
> >>>>endianness..." So which command do I need to add to which file to do
> >>>>this part?
> >>>>
> >>>>Thanks for your time.
> >>>>Ralph
> >>>>
> >>>>
> >>>>--
> >>>>-----------------------------------------------
> >>>>
> >>>>Ralph Jimenez, Ph.D.
> >>>>JILA/NIST and Department of Chemistry & Biochemistry
> >>>>440 UCB
> >>>>University of Colorado, Boulder
> >>>>Boulder, CO 80309-0440
> >>>>
> >>>>Tel: (303) 492-8439
> >>>>FAX: (303) 492-5235
> >>>>
> >>>>http://jilawww.colorado.edu/JimenezLab/
> >>
> >>--
> >>Ralph Jimenez, Ph.D.
> >>JILA/NIST and Department of Chemistry & Biochemistry
> >>440 UCB
> >>University of Colorado, Boulder
> >>Boulder, CO 80309-0440
> >>
> >>Tel: (303) 492-8439
> >>FAX: (303) 492-5235
> >>
> >>http://jilawww.colorado.edu/JimenezLab/
> >
>
>
> --
> Ralph Jimenez, Ph.D.
> JILA/NIST and Department of Chemistry & Biochemistry
> 440 UCB
> University of Colorado, Boulder
> Boulder, CO 80309-0440
>
> Tel: (303) 492-8439
> FAX: (303) 492-5235
>
> http://jilawww.colorado.edu/JimenezLab/ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078