Third Computer Lab:

Today sudents will self-explore at least two more advanced controls in Jmol:

Move and Surfaces

1. As before open your protein: Go to the Desktop to find :1xme.pdb1 (If not found, you will need to download it again. See last week.)

2. Open the Script Console if it doesn't open automatically. (File menu)

3. Link to Jmol scripting commands

4. Or go directly to move or moveto

5. Apparently, moveto is the newer version. You may try either one (or both).

6. Type something like this: move {followed by 9 to 11 numbers}

7. Second, read about surfaces here.

8. Demo page for testing surface commands

9. Test any other script commands on the list.

10. Rember how to save your molecule as is looks right now?

11. Type: write script /users/proteins/documents/1xme001.spt

12. The last part is the name of the file. It contains the pdb file number 1xme, a script number 001 in case you make different versions , and an extension .spt to indicate that this is a Jmol script file. Actually, you can call it anything, but I have found it advantageous to have a method for naming files.

13. The phrase " /users/proteins/documents "determines where the file is saved. Now check your documents folder to see if the file is there.

14. If the file is there, go back to the Jmol console and close the file. This can be done by typing: zap

15. Rember, you can retrieve the file by typing: script /users/proteins/documents/1xme001.spt