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This can be done with one command line (albeit a rather long one). Below is the code with (remove backslashes if pasting as a single line)  
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This can be done with one command line (albeit a rather long one). It also implies a rather recent version of awk, some older versions won't support the fixed width argument splitting.  Below is the code with (remove backslashes if pasting as a single line)  
    
grep 'ATOM\|HETATM' file1.pdb file2.pdb | \
 
grep 'ATOM\|HETATM' file1.pdb file2.pdb | \
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