More specifically, if we want to understand the different chains within a protein, is it enough to look at the fourth column of all the lines that start with "ATOM" in a pdb file, and see how many different chain identifiers exist there?


In the PDB format the lines with atoms can start either with ATOM or HETATM.

Chain ID is in column 22, i.e. it is 22nd character of a line that starts with ATOM or HETATM. (Programs that support 2-character chain IDs use columns 21-22 − it's a popular extension of the PDB format).

Yes, the number of different chain IDs is the same as the number of "chains" in the PDB file. But note that the "chain" from the PDB format is not necessarily a real chain (polymer). It may be a bunch of water molecules or something else.

  • $\begingroup$ Thank you for your answer. It’s less confusing now. $\endgroup$ – Yasmin Sep 30 '18 at 18:42

Your Answer

By clicking "Post Your Answer", you acknowledge that you have read our updated terms of service, privacy policy and cookie policy, and that your continued use of the website is subject to these policies.

Not the answer you're looking for? Browse other questions tagged or ask your own question.