VMD

General Description

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Home Page: http://www.ks.uiuc.edu/Research/vmd/

General Tutorials

• http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials

Cluster specific use

Prism

• Open an X11 terminal.
• From an SCS managed desktop (e.g., hostname is dskscs***.scs.fsu.edu) type:

qlogin -l vmd

• From all other machines first log in to pamd.scs.fsu.edu

ssh -Y pamd.scs.fsu.edu

• then type:

qlogin -l vmd

• This command logs you onto the least loaded prism node
• Type:

 vmd 

VisLab

• Open an X11 terminal.
• Matlab is installed locally on each VisLab machine so type:

 vmd 

Graphics Examples

• Example data files: http://people.scs.fsu.edu/~yuson/vmdexampledata.tar
• First step loading a molecule file
  

 1 Choose the File ! New Molecule... menu item  in the VMD Main window.

 2 Use the Browse...  button to find the file *.pdb( Protein Data Bank).

• Second step loading data into molecule
  

   1 Click on the name of the first molecule in the Main window molecule
   listing, then right click, choose Load Data Into Molecule...

 2 Use the Browse...  button to find the file *.dcd( contains atomic coordinates), load it.

• Exploring different drawing styles
  

 In the Draw Style tab  we can change the style  and color  of the representation. 

• Exploring different selections.
  

 Default choose all atoms. 

 After choose  nucleic.