How Do I Download Protein Monomers From Pdb?

Question

[kadhar]

Hi,

I would like to download protein monomers (one chain only) from pdb. I have an input file which contains PDB IDs. what is the easy way to download monomers from PDB?

[nabatifarzan90]

hi how can i get e6 protein human papiloma virus 3D structure from PDBank?

[GenoMax]

From this search. If you need introduction to PDB data then you can find that here.

Answer 1

[Pappu]

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.

[kadhar]

@pappu I tried your script. It only prints up to residue number 99 from all files. How can I get the atomic coordinates of residue's no >99?

[Pappu]

Can you tell me one of the pdb ids so that I can check?

[kadhar]

Please check this pdb ID 3QJ5.

[Pappu]

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

[kadhar]

Thank you for your comment. This code only prints the whole pdb file.

[Hamish]

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.