The project spec says to construct a grid over all the atoms in the PDB file, but it looks like using only the alpha carbons gives the correct output. Which method should we use?
Construct your grid using only the alpha carbons. I am confused by your recent emails about the “multiple chains” in example PDB files and don’t understand how this could count sites and nonsites multiple times for residues. Don’t the counts just keep track of how many sites and nonsites there were with that residue, and not how many times that residue occurred? Yes, the counts are only of the number of sites or nonsites that contribute a residue in a shell, and not how many times they contribute it. However, it is possible sometimes for PDB files to contain more than one type of protein (a complex of different proteins, for example), and it could be that the first chain in the file doesn’t contain a certain residue in a certain shell, but some of the others do, and so if you only read in the first chain you might get a different count of sites and nonsites than if you read all the chains. If you don’t understand what this means, it’s not terribly important for this project – just make
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