Jmol Training Session Part IV: Adding Side Chains

Opening your Model Design with a JPG File! To open your model design using your JPG file: Open Jmol Drag and drop the JPG file in the black model design box. Click “OK” in the width height box.

Opening Your Model Design with a Script File! To open your model design using your script file: Open Jmol Drag and drop the PDB file in the black model design box.

Opening Your Model Design with a Script File! To open your model design using your script file: Open the Console box. Click on “Editor”. Click on “Clear” in the Script Editor box.

Opening Your Model Design with a Script File! To open your model design using your script file: Copy and paste your script file from your word document into the Script Editor box. Click on “Run”. Click on “Console” to continue your model design.

Identifying Side Chains! How do you decide which side chains to highlight? There is more than one way to skin a cat! Check the Protein Data Bank Sequence Tab and examine the side chains that interact with the ligand. Read the Primary Citation and identify which side chains are highlighted. Examine the protein structure and the side chains that are most likely to interact with the ligand.

Identifying Side Chains! Question: According to PDB, which two histidine residues interact with the heme group? Answer: Histidine 63 and Histidine 92 To INCORRECTLY display sidechains Type – select :b and his63 Type – wireframe 1.0 Type – spacefill 1.25 Type – color cpk (More about “wireframe” and “spacefill” to come!)

Displaying the Side Chains! Why was this incorrect? Notice that you have the dreaded “bumpy backbone” This is a common error. AVOID THE DREADED BUMPY BACKBONE!

Displaying the Side Chains! Click the “UNDO” button until no side chain is displayed To CORRECTLY add a sidechain Type – select :b and his63 and (sidechain or alpha) Type – wireframe 1.0 (this gives “scaffolding” for the side chain) Type – spacefill 1.25 (this gives weight to the atoms in the side chain)

Coloring the Side Chains! To color only the side chain and not the backbone Type – select :b and his63 and sidechain Type – color cpk A common error is to color the backbone as well as the side chain. The “zebra backbone” may be avoided by following the commands listed above after you have added the side chain without the bumpy backbone. Now add the histidine 92 residue to your model!

Annotating Your Script Once you have created your script file, it is a good idea to make notes so that you remember why certain features of the molecule are highlighted and how you were able to highlight them. Any line that begins with the symbol # is ignored by Jmol. You can take advantage of this to add comments to your script. Use the comments to indicate what features of the molecule you are accenting in each of the blocks of commands. We call these blocks “cassettes”. After annotating your script, it is a good idea to run the script to make sure there aren’t’ any errors.

Annotating Your Script #DEOXY HUMAN HEMOGLOBIN_6-19-2017_1A3N   #Adding a Side Chain that Binds the Ligand (no bumpy backbone) #Initial Parameters background white select :b and his63 and (sidechain or alpha) backbone 1.5 cartoon off #Highlighting Only the B Chain #Coloring the Side Chain Without Coloring the Backbone restrict :b select :b and his63 and sidechain center:b color cpk #No Water Polka Dots #Adding a Second Side Chain Involved in Binding the Ligand restrict not water select :b and his92 and (sidechain or alpha) # Highlighting the Ligand select:b and hem spacefill 1.25 #Coloring the Second Side Chain wireframe 1.0 select :b and his92 and sidechain #Coloring the Backbone select:b and backbone color white select :b and helix color red

Your Fourth Assignment! Determine your model description information. Primary citation Authors (year published). Article title. Journal, Volume(Issue), Pages. Method Organism Resolution Deposition Date Ligands to highlight (and why) Sidechains to highlight (and why) Open your model design using the JPG file. Open your model design using the script file. Properly display the side chains in your model. No bumpy backbones! Properly color the side chains in your model. No zebra backbones! Save your model script file. Annotate your script.