Exons:
Bits of information for using the MUSC Shared Resource,
the BioMolecular Computing Resource (BCR).

Exon_44 Running the SYBYL TRIAD and the SGI version of VNMR 
and running VNMR remotely from the NMR SUN workstation at MUSC.

Running the SYBYL TRIAD software for analysis of NMR data
is quite easy. Start SYBYL in the usual way by typing:
setsybyl
setunity
sybyl

Then under the "option"  menu select "TRIAD". This will launch
a popup window within which you may read files and start NMR analysis.

Connecting to the VXR SUN workstation remotely using x-server
software.

CASE 1:If you have an WINDOWS PC and eXceed, follow these steps.
          
This has already been configured on the BCR Dell.
          
In the exceed folder launch Xstart.
          
In the popup window, enter "128.23.41.245" as host
          
Select SUN as the host type.
          
Click on the ellipsis (the "..." button) and select
          "xterm". Repeat and select OpenLook Window Manager
          
Click on the "login info" button and enter your choice for the window name.
          
 Next double click on "run", login
          
 This should open an xterm window and turn on OLWM
          
 Finally type "vnmrx &" and you can start your analysis.
CASE 2:If you have a MAC OS PC and eXodus, follow these steps.
           
 eXodus provides a resource file which must be properly
               placed into your SUN directory. The file is called
               ".eXodusSunrc".Once on the SUN in your directory you 
               must type "chmod a+x .eXodusSunrc". This get the
               SUN set up to handle your eXodus logins.
           
The set up process for using eXodus to talk to a SUN
              computer is described in the eXodus manual.Basically you have
              to move some files from a Sun_OpenWindows_Support folder
              to the Connections folder of eXodus on your MAC (referring 
              here to version 6 set up).
           
When you start eXodus, go to the Edit menu and select Server.
              In the popupwindow, select Screens and for Type select rooted.
              Under Keyboard Mapping select MacIntosh and select both
              command and option keys to macintosh as well. Next go to 
              Mouse Buttons. For Button 1 select Mouse only. For button 2
              select mouse AND command. For button three select mouse and
              option.
           
Under the  CONNECTIONS menu select Connection Manager. In the
              popup window select Sample xterm, then duplicate, then edit.
              Fill in the title, for host enter "128.23.41.245". Click on Prompt
              when connecting. Select rexec and in the command line type
              .eXodusSunrc $$ME$$ xterm -ls -sb -fg blue -bg gray -g 80x24+100+100
           
Finally click on connect. When you see the SUN UNIX prompt type
              "olwm &
               vnmrx &"
              This should start the VNMR software.
           
Mouse button 1 is executed by mouse alone. 
              Button 2 by simultaneously pressing command and the mouse 
              Button 3 by simultaneously pressing option and the mouse.
              Experiment with the key and mouse combinations to produce
              various cursor effects. 
CASE 3:If you have a MAC OSX
           
 Download or otherwise activate X11.
           
 Start an X11 terminal window. Type "xhost + 128.23.41.245".
           
 Type "telnet 128.23.41.245". Login with your VNMR username and password.
           
 Select "s" as the terminal type.
           
 Type "who" note the response indicating your login eg jane  janespc.deptxyz.musc.edu
           
 Type ".eXodusSunrc janespc.deptxyz.musc.edu:0.0 xterm -ls -sb -fg blue -bg gray -g 80x24+100+100"
           
 Type "olwm &" then type "vnmrx &" and your session should proceed as before.        
Running VNMR on the SGI workstations at the console or via x-server
software from your remote PC.

 Modify the .4Dwmrc file in your personal root directory.
    
 Modify the .cshrc file in your personal root directory.
         
You will need to add this line:

          source /usr/common/bcr/vnmr2001/startupVNMR.csh

    
 Create a sub-directory in your personal root directory
         called "vnmrsys".
    
 Within the vnmrsys sub-directory add a file called "global"
    
 Within the vnmrsys sub-directory, create sub-sub-directories
         called "maclib" and "exp1".
    
 Log out and log back in.
    
 FTP your data files from your SUN account space to your homeroom.
         In particular put the files into the expX directory of your vnmrsys
         subdirectory where X is a number like 1 or 2 or 3 etc.
    
 Start VNMR from the x pulldown menu or at the
         command line type  "vnmrsgi &"



The BCR at the Medical University of South Carolina

 URL: http://bcr.musc.edu/

  Last modified: February 11, 2004- ESH 



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