PDB Tutorial: consistent variable names; fix quotes

Doc/Tutorial/chapter_pdb.tex

@@ -12,17 +12,17 @@ \subsection{Reading a PDB file}
 
 \begin{verbatim}
 >>> from Bio.PDB.PDBParser import PDBParser
->>> p = PDBParser(PERMISSIVE=1)
+>>> parser = PDBParser(PERMISSIVE=1)
 \end{verbatim}
 
 The {\tt PERMISSIVE} flag indicates that a number of common problems (see \ref{problem structures}) associated with PDB files will be ignored (but note that some atoms and/or residues will be missing). If the flag is not present a {\tt PDBConstructionException} will be generated if any problems are detected during the parse operation.
 
-The Structure object is then produced by letting the \texttt{PDBParser} object parse a PDB file (the PDB file in this case is called 'pdb1fat.ent', '1fat' is a user defined name for the structure):
+The Structure object is then produced by letting the \texttt{PDBParser} object parse a PDB file (the PDB file in this case is called \verb|pdb1fat.ent|, \verb|1fat| is a user defined name for the structure):
 
 \begin{verbatim}
 >>> structure_id = "1fat"
 >>> filename = "pdb1fat.ent"
->>> s = p.get_structure(structure_id, filename)
+>>> structure = parser.get_structure(structure_id, filename)
 \end{verbatim}
 
 You can extract the header and trailer (simple lists of strings) of the PDB