BIOL 6312: Proteins
Lesson 3: February 13
1. Find the file "Jmol.jar" file in the jmol folder. Double click this icon.
2. Drag the window to the left side of the screen. If necessary, make the window larger by dragging the lower right corner.
3. Go to the "File" menu at the upper left of the Jmol window, and click on "Console". You should see a new window.
4. Position the windows as before.
5. At the upper left, under the Jmol "File" menu, click "Open"
6. Look for the "pdb_files" folder and open it.
7. Now you should see the "1xme.pdb1.gz" file. Open it.
Or, type "load pdb_files/1xme.pdb1.gz" into the Console.
8. Now you should see the protein appear in the window.
9. To change the appearance of the molecule, in general, you must first "select" something, and then "render" it, e.g by color.
10. To color the protein by "structure", means alpha helices are magenta, beta-strands are gold, etc. Type "select all" or "select protein" . Now type "color structure". To color each chain differently, type "color chain". To color by rainbow colors, type "color group". Now the N-terminus is blue and the C-terminus is red.
11. Now go back to color by chain. Drag the molecule around so that you can see the three different chains. One is pale blue, one is pale green, and one is pale pink.
12. Perhaps you do not like these colors. Type "select :a; color red"
You can separate commands by a semi colon ; rather than hitting "return" each time.
13. Now change the colors of chains b and c. Many names of colors are recognized by Jmol. e.g, salmon, deeppink, darkblue, lightblue, etc. Colors can also be written according to RGB: [255,255,255] which is white. Any 3 numbers between 0 and 255, gives you over 16 million shades of color. Or by [xFFCC00], which is a shade of yellow. (where each digit can be A-F or 0-9, so-called hexadecimal).
So, "color lime", "color [x00FF00]", or "color [0,255,0]" all do the same thing.
Jmol can use standard colors for each chemical element, or for chains. See the link to Jmol colors: http://jmol.sourceforge.net/jscolors/ You can see that the blue used in "color by chain" is actually [192,208,255] or [xC0D0FF]
14. Now change chain c to backbone: Type "select :c;cpk off;cartoon off;backbone"
Or: "select :c;backbone only"
Backbone does not trace the backbone atoms, but provides one centered point for each amino acid at the alpha carbon (CA). "Trace" is similar to backbone but provides a smooth curve."Wireframe" traces the 3 backbone atoms, along with the sidechains. One way to show the actual backbone is to type "wireframe only;select backbone;display selected"
15. This backbone is very thin, so type "wireframe 80". Or just hit the up arrow. You will see the backbone command re-appear. Leaving a space, type "80".
Trial and error will quickly get you the thickness you want. For cpk, you can use %, e.g. 80%. If you use just 80, it is a different scale and gives you tiny spheres.
Ball-and-stick is a combination of cpk (or spacefilling) and wireframe. Try it out by typing "spacefilling 20%; wireframe 40". Or "cpk 20%; wireframe 40"
16. Now select the leucine residues in chain c by typing "select leu:c" or "select leu and :c"
17. Now color these residues a different color. Then type "wireframe 100"
18. To select residue 4 in chain c, type "select 4:c"
19. Then type "cpk;color cpk"
20. now select chain a by typing "select :a"
21. Type "cpk off" the cartoon should still be there.
22. Now select the two hemes: Type "select hem or has"
23. Note the Boolean logic. (if you type "hem and has" you will get no atoms, since no atom can be in two different groups at once.) Now type "cpk;color cpk"
24. A useful command "display selected" Done now it should hide the a,b and c chains, and show only the two hemes. "display all" brings it all back.
"display not selected" is also valid. Or "hide selected" or "hide not selected"
25. Now try other things on your own. At anytime type: "write image png "1xme5.png" ". Or, for jpg files: "write image jpg 1xme5.jpg". For high resolution, type "write image jpg 1000 1000 "1xme7.jpg"
This will write a graphic file in png or jpg format to your jmol folder. It has the special feature that if you drag and drop the file to a Jmol window, you can modify the file further. Magical!
I believe that the image file must be in the same folder as the pdb file. So type: "write image jpg pdb_files/1xme6.jpg"
Or type "script 1xme5.png" or "script pdb_files/1xme6.jpg" and the structure should also reappear.
Remember to type "zap" to get rid of the current structure.
26. You can also select using these expressions: protein, nucleic, dna, rna, amino, mainchain, sidechain, helix, sheet, hetero, solvent, water, hetero and not water
27. See http://chemapps.stolaf.edu/jmol/docs/?&fullmanual=1&ver=14.4 for a complete listing and explanation of all commands.
28. Or check this page for examples: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
29. If I am working on a project to make images or video of a protein, I usually download a new version of jmol, then download the pdb file(s) to that same folder. Then there is no issue of jmol finding the pdb file or saved image files.
Comments/questions: email me
Copyright 2018, Steven B. Vik, Southern Methodist University