How Do I Download Protein Monomers From Pdb?
1 answer
I answered the same question How To Download Atomic Coordinates For A Specific Chain From A Pdb File?. Please look at previous posts before posting new questions.
You have to remove one space after A: ' A ' . Look at grep manual..
for i in 3QJ5; do wget -c "http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId="$i -O $i.pdb; grep ATOM $i.pdb | grep ' A ' > $i_A.pdb; done
PDB ATOM records are not delimited, so the solution suggested by Pappu will not work for all PDB entries. I suggest you see the How To Download Atomic Coordinates For A Specific Chain From A Pdb File? for an option which takes this into account.
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