1. Jmol Training Session Part IV: Adding Side Chains

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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!)

8. 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!

9. 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)

10. 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!

11. 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.

12. Annotating Your Script
#DEOXY HUMAN HEMOGLOBIN_ _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

13. 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.