Preparation and familiarization with basic features

1. Download structures from Protein Data Bank (PDB)
   Go to the RCSB (Research Collaboratory for Structural Bioinformatics site of Rutgers/SDSC Protein Data Bank (PDB) depository URL http://www.rcsb.org/pdb/
   • Download structures:
     1MBN and 1A6G (carbonmonoxy mygolbin from sperm whale)
     1GDI (carbonmonoxy leghemoglobin from yellow lupin)
     1CDE (GART, GlycinAmide Ribonucleotide Transformylase, high pH, with bound substrate and pseudo-cofactor)
     1GAR (dimeric GART, low pH, with bound inhibitor)
     3GAR (E70A GART, high pH, substrate-freee)
     2GAR (E70A GART, low pH, substrate-free)
     1GHQ (complex of complement receptor 2 with C3d)
2. Familiarization with SPDBV toolbar, windows, buttons, and pulldown menus
   Load Deep View/Swiss PDB Viewer by clicking on the icon
   The Tool Bar will be loaded, Pull Down Windows are at the top, Buttons are at the midddle and additional information is at the bottom
   Load PDB file 1A6G
   The Main Window (or Display Window) with the structure is opened and a Loading Information Window is opened
   The Information Window is opened upon loading the structure and contains useful information - close it because you will not need it any more
   In the Tool Bar under Windows click and open the Control Panel , the Alignment Window , the Layers Info Window , and the Ramachandran Plot Window
3. Spatial manipulation buttons of Tool Bar
   1st button: center
   2nd button: move
   3d button: zoom
   4th button: rotate
4. Preferences
   In Tool Bar click on Preferences and then General, Loading, etc
   These are certain functions that the Deep View can do upon loading the protein
5. Molecular graphics
   Familiarization with different types of molecular graphics of SPDBV
   For the moment keep only The Main Window, the Toolbar, and the Control Panel
   Familiarization with Control Panel
   There is a header with the structure PDB code, a subheader with 3 buttons, and a list with a title and 8 columns
   • 1st column: Secondary Structure and Residue Name and Number
     click on residues - they turn red when they are selected - drag the cursor down for multiple selections
     For an alternative and useful way for selection, in Tool Bar, click on Select All and Select None
   • 2nd column: Show Backbone
     click on check marks, single and multiple, look at the structure
     Hide all backbone by selecting "None" and clicking on List Title at "Show Backbone"
     Display all backbone by selecting "All" and clicking on List Title at "Show Backbone"
     Note that all residues remain selected (red) - you may need to unselect them depending on what you are planning to do
   • 3d column: Show Side Chain
   • 4th column: Show Label
   • 5th column: Show Dot Surface
     Click at the little arrow to see the options for ssurface calculation
     In Tool Bar click on Preferences Surfaces for preferences when loading the protein
   • 6th column: Show Ribbon
   • 8th column: Coloring Options
     Click on the little arrow ro see options for coloring the various parts of the protein - select one
     The same function can be accomplished in Tool Bar by clicking on Color Act on ...
   • 7th column: Show Color
     Play a little with these options
6. Coloring oiptions
   In Tool Bar click on Color and try the various options
7. Coloring preferences
   In Tool Bar check the color preferences
   The following conventions are used
   • background: black
   • Atoms
     C: white
     H: black
     N: blue
     O: red
     S, P: yellow
     Other: grey
   • Bonds
     S-S bridge: yellow
     Strong H-bond: green
     Weak H-bond: light green
     van der Waals clashes: magenta
   • Residues - the following conventions are standard in structural biology and I prefer them from the Deep View default ones
     Acidic: red
     Basic: blue
     Non-polar: green
     Polear: grey
   • Structures - these are personal preferences not conventions
     Helix: red (or yellow in black background)
     Strand: cyan
     Other: grey
8. Save Projects or picture files
   in Tool Bar, click on File , Save
   Layer is the current layer containing one protein
   If a second protein was loaded there will be 2 layers present. These can be saved individualy or as a project
   Selected residues can also be saved separately
   Images and stereo images
   Other, like surfaces, electrostatic potentials (take a long time to compute), alignments, Ramachandran Plot values, etc.
9. Remove protein
   In Tool Bar click on File , then Close

Back to Main Page