VMD-L Mailing List

From: Ralph Jimenez (rjimenez_at_jila.colorado.edu)
Date: Tue May 08 2007 - 22:38:01 CDT

Gentlemen,
  Thanks for your help. I opened a bash shell window where I created the .bashrc
file and linked it to .bash_profile as suggested by Dan. I then opened VMD and
ran the puts "$env(VMDMSMSUSEFILE)" command at the VMD prompt, to which it
returned "1", which I guess means the variable is found.
  However, when I select the msms drawing method from the graphical
representations, it doesn't work, and gives me this error:

sh: line 1: msms: command not found
ERROR) Cannot read MSMS facet file: /tmp/vmdmsms.u501.534.face
Info) Could not compute MSMS surface
Info) Done with MSMS surface.
RCNE SendEventToEventTarget (suom Moved ) failed, -50

  I verified that msms is in the directory where VMD starts.
Ralph

Dan Wright wrote:
> You may need to have these commands in a file called .bash_profile
> rather then .bashrc. bash will source one or the other of these files
> depending on how it is called; to solve the problem so you don't have to
> worry about it, run "ln -s .bashrc .bash_profile" to make a symbolic
> link .bash_profile -> .bashrc.
>
> Dan
>
> 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/