Class Project
Revision 1.1
Septemeber 12, 2025

Your job is to create a report that can be used to teach about structure in general and about your protein in particular. You will construct documents that you can use to illustrate and explain the your protein at the level of bond distances, angles and torsions, hydrogen bonds and other molecular interactions (including the hydrophobic effect), secondary elements and their interactions, catalysis, function, dynamics and evolution. You cannot do all of this, but should focus on some aspect that interests you. The documents can be word and powerpoint.  

For your project you will use Illustrator, PyMol, Endnote and online programs. Ensure you have the required software installed on your computer.

Create a directory for this project with the following subdirectories

figures
	illustrator
	jpeg
endnote
pymol
literature
misc

Download the coordinates of your protein into the pymol directory. Open PyMol and use 'cd' to navigate to your PyMol directory. [If you have never done this before you will need instruction from the professor or another student]. Become familiar with the unix commands cd (change directory), ls (list the contents of the directory) and pwd (present working directory).

Start by using PyMol to characterize/confirm the fold and the general shape. First you can color it by secondary structure and stare at it. 

Once the directory is set in PyMol and the PDB file is downloaded, in PyMol type (or edit the zzzz and copy and paste) 

load zzzz.pdb, myprotein   		
	# loads coordinates and creates object myprotein
hide everything, myprotein 		
	# turns off all representations
show cartoon, myprotein 		
	# turns on cartoon representation
color salmon, ss h and myprotein   
	# helices
color yellow, ss s and myprotein   
	# beta sheets
color grey70, ss l and myprotein   
	# loops/coil


Once those commands work, open a file and paste your commands into it. Then paste the header commands (at the bottom of this file) immediately preceeding (before) the load command. Save the file in the pymol directory as myprotein.pml. Type ls to ensure your file is in the right place. Copy and paste the contents of myprotein.pml into the PyMol command line to ensure everything works. 

Use @myprotein.pml to run your PyMol script within PyMol

Google Scholar. Perform google scholar search and find seminal papers describing the structure and function of your protein. Download those papers into Endnote, and save the endnote library in the endnote directory. Save the pdfs of the papers in the literature directory. 

Start to make images of isolated secondary elements (helix, sheet, turns).


#----------------------------------------------------------------
## PyMol Header by Loren Williams##

# delete all objects and reset pymol
reinitialize
# set the background color to white
bg_color white
# make the background transparent for ray trace 
set ray_opaque_background, 0
# set the ray trace mode
# normal color
set ray_trace_mode, 0
# normal color + black outline
#set ray_trace_mode,  1
# black outline only
#set ray_trace_mode,  2
# turn off shadows during ray trace
set ray_shadows, 0
# set the mouse mode for laptop
config_mouse one_button
# get rid of double bonds and skinny bonds to Hydrogens
set stick_h_scale, 1
set valence, 0
# high quality surfaces
set surface_quality, 3
## End PyMol Header
#----------------------------------------