Jmol Training Session Part II Downloading Jmol and

Let’s Begin Jmol: Create a Folder! • Create a folder on your desktop to

Download the Correct Version of Jmol! Be sure to use the correct version of

PDB File Search! You may search by: • Molecule name • Scientist name •

PDB File! • Type the file name in the search bar. We will use

PDB File Authors! • Type the file name in the search bar. We will

PDB File Organism! • Type the file name in the search bar. We will

PDB File Method! • Type the file name in the search bar. We will

PDB File Download! • Click on the “Download File” button. Download File

PDB File Download! • Click on the “PDB Format” button in the dropdown menu.

Opening Your File in Jmol! • Open Jmol. jar from your folder (double click)

Opening Your File in Jmol! • Your screen should look something like this: Model

Opening Your File in Jmol! • Drag and drop the PDB File into the

Move Your Model! Try these “Mouse Gestures”!

Begin Your Design! Type commands in the console box. • To change the background

Your Second Assignment! 1. Select one of the posters from PDB 101. We will

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Jmol Training Session Part II: Downloading Jmol and PDB Files

Let’s Begin Jmol: Create a Folder! • Create a folder on your desktop to store the information needed to design your model. • Include a copy of Jmol. Copy and paste a copy of the Jmol. jar file into the folder you created. http: //cbm. msoe. edu/crest. Jmol. Resources. php • Include the pdb file of the protein to be modeled. (more instructions on this step to follow)

Download the Correct Version of Jmol! Be sure to use the correct version of Jmol! We will not be able to view your files if you use a version other that the one specified! This year we will use version: Jmol 14. 15. 3

PDB File Search! You may search by: • Molecule name • Scientist name • File name (a four character code) Search Bar

PDB File! • Type the file name in the search bar. We will use 1 A 3 N. File Name

PDB File Authors! • Type the file name in the search bar. We will use 1 A 3 N. Authors

PDB File Organism! • Type the file name in the search bar. We will use 1 A 3 N. Species

PDB File Method! • Type the file name in the search bar. We will use 1 A 3 N. Method

PDB File Download! • Click on the “Download File” button. Download File

PDB File Download! • Click on the “PDB Format” button in the dropdown menu. • Save the file in the Jmol folder you created on your desktop. Download File

Opening Your File in Jmol! • Open Jmol. jar from your folder (double click)

Opening Your File in Jmol! • Your screen should look something like this: Model Design Box Console Box: Type your commands here.

Opening Your File in Jmol! • Drag and drop the PDB File into the black screen.

Move Your Model! Try these “Mouse Gestures”!

Begin Your Design! Type commands in the console box. • To change the background color: Type - background white (you may want to try a few other colors)

Your Second Assignment! 1. Select one of the posters from PDB 101. We will print it for you! 2. Download each of the three PDB files you previously identified into the folder your created on your desktop. 3. Open each of these files in Jmol. 4. Practice moving the model with either your mouse or touchpad. Keep in mind “mouse gestures” will vary if you have a Mac. 5. Practice typing commands in the console box by changing the background color of your model designs.