VMD-L Mailing List

From: Ralph Jimenez (rjimenez_at_jila.colorado.edu)
Date: Tue May 08 2007 - 14:15:54 CDT

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/