Biol 6312

10 April 2018

Lesson 9: Showing conservation in Jmol with ConSurf

Today we will see how to use the ConSurf server to obtain an alignment of protein sequences, colored by conservation, and how to color a Jmol version of the protein in the same way.

I suggest not trying the ConSurf server today, but rather, just look at my results. Later, for your project you should consider using ConSurf.

1. Identify a protein and its PDB ID number. (not needed for today)

2. If the protein is a multi-subunit protein, you should select one chain to analyze, e.g., :B

3. Go to the ConSurf webpage: http://consurf.tau.ac.il/2016/

4. I recommend, later, to look at the Menu tabs: Overview, Quick Help, and FAQs

5. For now, check the "Amino-Acids"

6. Is there a known structure? Yes

7. Type in the PDB code, click "Next"

8. If the file has more than one chain, you will need to select one from the pull-down menu

9. If you have no Multiple Sequence Alignment (MSA) click "No".

10. Use the default values, and select "Automatically"

11. You can use the default values for the remaining choices.

12. Near the bottom, you should give the job a name, e.g., the enzyme name or pdb code

13. Type in your smu email address, so they can send you a link to the results. It might take one hour or longer, depending upon the number of recent requests.

14. For today, here is the link for my recent results:

http://consurf.tau.ac.il/results/1523213939/output.php

15. Scroll down to

ConSurf calculation is finished:

Final Results

16. You can view the results quickly, in two ways:

View ConSurf results with NGL viewer

View ConSurf results with FirstGlance in Jmol

17. Just below is a link to download all the results

• Download all ConSurf outputs in a click!

18. After downloading it, open the zip file.

19. To see the sequence alignment, double click the file: "Multicolored_MSA.html" to open in a broswer.

20. To examine the conservation in Jmol, copy two files into your jmol folder:

1h0l_ATOMS_section_With_ConSurf.pdb

rasmol.scr

21. The first is a pdb file for the protein, and the second is a script file that colors it

    Now, open Jmol.jar

22. Open the console from the "File" menu. Change Background to White

23. From the File menu open the new pdb file: 1h0l_ATOMS_section_With_ConSurf.pdb

24. To see the ConSurf colors Type: "script rasmol.scr"

(To see what is in the script file, open it in a text editor.)

25. Once you see the coloring, you might want to switch back and forth between "cartoons only" and "cpk only"