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Visualizing Docking using UCSF Chimera - English

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Outline:
Open the PDB file for the receptor on the Chimera interface.
Select and delete, ligand, water and glycerol molecules from the receptor structure.
Add the most preferred docking pose of ligand to the receptor structure.
Show hydrogen bonds and change the color of the bonds.
Show hydrogen bond length and energy.
Show non-bonding interactions and  change the color of the pseudo-bonds.
Highlight the active site residues, change their display format and color.
Show the surface for the receptor-ligand complex  colored by the amino acid hydrophobicity.
Show the interior of the binding pocket using the Viewing Controls in the tools menu on Chimera interface.
Width:1036 Height:676
Duration:00:15:55 Size:12.7 MB

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Pre-requisite

Analyzing Docking Runs

  Assignment

Code files

  • Code-files-Visualizing-chimera/
  • Code-files-Visualizing-chimera/2vta.pdb
  • Code-files-Visualizing-chimera/ligand-conf1.pdb
  • Code-files-Visualizing-chimera/ligand-conf2.pdb

Script

Slides

  • Slides-Visualizing-Chimera/
  • Slides-Visualizing-Chimera/Visualizing-Chimera.tex
  • Slides-Visualizing-Chimera/st-logo-new.png
  • Slides-Visualizing-Chimera/Visualizing-Chimera.pdf