Required Powerpoint Report (2016)

You will not present your Powerpoint to the class. Your Powerpoint report will be graded, but it is not a test. It will simply be a record to document your practical work and understanding. You are encouraged to discuss your work with other students and ask for help from the instructors.
Email your Powerpoint files to martzeric@yahoo.com. (You may also use emartz@microbio.umass.edu but there may be problems sending attachments to that address.)
If you choose a homology model, email that homology model to me. It can be zipped. Or you can send me a dropbox link.


ConSurf Server Procedure.
Use this for Question 14, only if the instructor is not available for guidance.
  1. Go to the ConSurf Server.
  2. Select Amino Acids.
  3. Check YES there is a known protein structure.
  4. Enter the PDB code, or upload your homology model (or biological unit).
  5. Select a chain for analysis. ConSurf can analyze only one chain at a time.
  6. Check NO, you will not be uploading a multiple sequence alignment. (ConSurf will create one for you.)
  7. Leave all parameters at their pre-set defaults. (If you want a research grade result, check "Let me select the sequences for the analysis manually out of BLAST results", and see Limiting ConSurf Analysis to Proteins of a Single Function.)
  8. Enter your email address at the bottom of the form (this is important so you don't lose your results). Optionally enter a job title.
  9. Click the button Submit. It may take an hour or more to complete this calculation.
  10. When it is finished, click the button to view the results in FirstGlance.
  11. Include the web address of the ConSurf result in your report!