VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 08 2007 - 13:44:43 CDT

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/ 

-- 
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