Friday, February 15, 2019

Molecular Graphics Models using Swiss PDB Viewer

locBLAST Input

This tutorial presents various models of molecular graphics representations such as Wireframe model, Ball & Stick model, Spacefill model, Surface model, Stick model, Backbone model, Van der Waals model, Ribbon model, Strand model, and Electrostatic potential model of protein structure using Swiss PDB Viewer.

Protocol

  1. Open Swiss PDB Viewer software.
  2. Click File Open PDB File… menu to browse protein structure (.pdb file) location. By default, it displays protein structure in “Wireframe” model.
  3. In Control Panel window, right-click symbol “::v” to display whole protein structure in “Van der Waals” model.
  4. Click Display Render in Solid 3D menu, and click Display Show Backbone Oxygens menu (deselect) to display protein structure in “Sticks” model.
  5. In Control Panel window, right-click symbol “side” to display whole protein structure in “Backbone” model.
  6. In Control Panel window, right-click symbol “ribn” and “show” to display whole protein structure in “Ribbons in Cartoons” model.
  7. Click Color  act on Backbone + Sidechains act on Ribbon menu to display ribbons in secondary structure color.
  8. Click Prefs 3D rendering… menu to open 3D rendering parameters window. In Bonds section, change Radius (solid) to “0.150” Å and Smoothness (1..13) to “13”. In Atoms section, change Radius to “0.400” / 30, Atom Smoothness (1..13) to “13”, and Spacefilled atom smoothness (1..13) to “13”. The protein structure will be displayed in “Ball & Stick” model.
  9. In Control Panel window, right-click symbol “::v” to display whole protein structure in “Spacefill” model.
  10. Click Prefs Ribbons… menu to open Ribbons Preferences window. De-select Render as Solid ribbon checkbox to display protein structure in “Strands” model.
  11. In Control Panel window, right-click symbol “::v”, “ribn”, and “labl” and clear selection, to reset display to “Ball & Stick” model. Again, click Display Render in Solid 3D menu to reset display to “Wireframe” model.
  12. Click Prefs Surfaces… menu to open Surface Preferences window. In General Appearance section, select Filled Triangles (only in 3D mode) and Quality [1..6] to “6”. In Default surface Color: section, select Electrostatic Potential and click ‘OK’ button. Click Tools Surface Compute to display protein structure in “Molecular Surface” model.
  13. Click Tools Surface Discard menu to reset display to “Wireframe” model. Now, click Tools Compute Electrostatic Potential, and click Tools Triangulate Current Map and accept changes to display protein structure in “Electrostatic Potential” model.

Brief Video Tutorial

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