Visual Molecular Dynamics（VMD）

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VMD

• Powerful tool for molecular visualization and analysis
• Theoretical and Computational Biophysics group at University of Illinois at Urbana-Champaign

cat ~/.vmdrc

After everything is initialized, VMD reads the startup file using the equivalent of the command play .vmdrc.
This file contains text commands for VMD to execute just as if they had been entered at the console.

#mol default style VDW
color Display Background black

#add personalized keyboard shortcuts
user add key o {display projection orthographic}
user add key p {display projection perspective}

#position and turn on menus
menu main on
menu graphics on
after idle {
after 2 {
menu tkcon on
#pbc box
 }
}

#set default representative
mol rep VDW ;
mol selection "nucleic" ;
mol addrep 0 ;
mol rep CPK;
mol selection "resname BCDC" ;
mol addrep 0 ;


lappend auto_path /usr/share/tcltk/tcllib1.17
lappend auto_path /home/xtong3/vmd-scripts/la1.0
lappend auto_path /home/xtong3/vmd-scripts/orient

Tcl Built-In Commands

• NAME
  lindex - Retrieve an element from a listSYNOPSIS
• lindex list ?index…?DESCRIPTION
  The lindex command accepts a parameter, list, which it treats as a Tcl list. It also accepts zero or more indices into the list. The indices may be presented either consecutively on the command line, or grouped in a Tcl list and presented as a single argument.

Generate high quality figures

VMD render:
follow the instruction on http://www.ks.uiuc.edu/Training/Tutorials/vmd-ref/imgmv/tutorial-html/imgmv-tutorial.html
axes off
water -transparent
save visualization state: *.vmd
save as *.tga file

Use Gimp to edit:
crop / erase unwanted part
set resolution to 300, width 945 pixel( or pel)
export as *tif

Steps:

1. Change background to silver, adjust other settings such as color of atoms, size,material.
2. Save visualization *.vmd for future use. You can edit it, find and change the information for new system .Such as change infile_name.gro and other selections
3. File - Render - (scene using Tachyon and add “-res 2800 1500” at the end of render command
4. Blow up the visualization window and zoom the content as much within everything you need can be seen.
5. Start rendering
6. Use software GIMP - image - autocrop
7. Image - scale - change size unit to inches, modify resolution to 300*300 pis/in.
8. Export as *png