Patricia L. Clark & Elizabeth
Klimek
last updated: November 9, 2001
1. Download and install Swiss PDB Viewer program: http://www.expasy.ch/spdbv/
2. Download PDB file of interest; unzip if .zip file
3. Start Swiss PDB Viewer program
4. Open PDB file (at startup, or under “File”)
5. Several windows will
open (or open them manually under “Wind”):
- input log text file (I usually close this immediately; but it may show info
on missing
atom locations, etc.)
- toolbar (should be small window across top of screen, with several small boxes
- main window (should show protein in some format)
- control panel (long narrow window to right of main window, with sequence and
boxes)
6. To adjust the molecule display:
Setting the background
color
Prefs > Colors > Background (button)
choose new color from window
Turning side chain display
on/off
in Control Panel, find residue of interest
click check mark under “side” to turn off side chain display; click
again to turn on
NOTE: must have backbone display on to display side chain!
on Mac, hold “Option” key and click anywhere under “side”
to turn all side chains on/off
Turning backbone display
on/off
as above for side chain display, but use the check marks under “show”
Coloring specific residues
in Control Panel, find residue of interest
make sure pulldown menu under “col” (accessed through black triangle)
is set to “backbone + side”, or whatever you desire to color
click box for appropriate residue, under “col”
select new color in window
Drawing ribbons
in Control Panel, select all residues under “ribn” (Option-click on
Mac)
under “col” pulldown menu, select “ribbon”
color all residue boxes desired color for ribbon (see above, Coloring specific
residues)
Ribbon properties
Prefs > Ribbons
Drawing in 3D
Making a surface
---making a surface for a single amino acid residue
Adding labels
“Hiding” part of the protein
7. Manipulating the protein structure:
Rotating the protein
Moving (translating) the protein
Zooming in and out
8. Advanced techniques:
Defining the point of rotation
Displaying and working with multiple structures in one field
---Changing which structure is “active” for selections
---“Locking” 1 or more proteins in a field
Using lights
Aligning structures
9. See the User Guide for more information: http://www.expasy.ch/spdbv/text/main.htm