Conservation scoring 2: mapping conservation onto a protein structure  
For the impatient: click here to go straight to the results page.
Assuming you have succesfully mastered mapping conservation onto HPPD sequence, lets take a look at mapping the information onto the structure. Download the example directory, if you haven not done so yet (left click, or right click to save to preferred location, save and unzip). Find the file with the alignment of sequences homologous to HPPD (refseq_search.afa) and upload. Using a pre-aligned set of sequences will make things go a little faster. You can leave the Reference Sequence field empty. Upload the structure 1sqi.pdb provided in the directory, choose the chain A, and click submit.
Notice that in among the Downloadables you now have something called "pymol session file." PyMol session (which you will have to unzip after downloading) is a file readable by PyMol. If you have PyMol installed, find the downloaded file (it should have the extension "pse") in the File->Open menu. If you do not have PyMol installed and/or do not know how to further manipulate the visualization there, you can start from the PyMol links on the visualization help page.
Do not have your own set of sequences?
Not happy with the alignment produced by the server? Read here about re-aligning sequences by yourself.