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  • yes, you are correct, I edited my question. Yes, the white space has to be maintained, that's the thing Commented Apr 17 at 17:25
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    And what do you want to change A to in the 5th column? To B? Please be explicit. Why are some changed and others not? For example, I see ATOM 3674 CD1 PHE A 460 in your output. Why is that A and not B? And is there one TER or many? Which one should we use? Commented Apr 17 at 17:26
  • I only would like to change the 5th column which corresponds to the protein chain ID, the other As need to stay as they are Commented Apr 17 at 17:30
  • I really don't think PDB files are tab-delimited, by the way. For example, see rcsb.org/structure/9K38. That isn't tab-delimited. Not even the ATOM lines are tab-delimited: sed -n '/\t/p' 9k38.pdb | wc -l returns 0. I think you're just used to seeing the columns aligned, but you likely don't have tabs in your actual file. Commented Apr 17 at 17:46
  • you might be right, they are aligned like in a tab but the separator is not /t, it is a "fixed-width columns" separator, but the POSIX works Commented Apr 17 at 17:55