I'm a student currently looking at antibody responses against a viral target protein of interest.

I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody structures that bind to this protein and rougly know whereabouts it binds. I would like to know if it is possible to combine these two structures into a single session to observe or at least overlay the two structures together. Many thanks!

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    $\begingroup$ You might find a PyMol expert on this list. If not try SE Bioinformatics or even Chemistry. $\endgroup$
    – David
    Jun 12, 2020 at 14:08
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    $\begingroup$ I don't think PyMOL has built-in functions for that; you might have to use a docking software like AutoDock. I'd also recommend asking on Bioinformatics SE as David suggested $\endgroup$ Jun 13, 2020 at 15:32

1 Answer 1


Multiple structures may be read into a given session using the following for each pdb:

File -> Open

In the narrative below, the reference antibody has the name AAA and the second antibody has the name BBB. The heavy and light chains have pdb chain IDs A and B, respectively. Adjust those as needed.

Whole molecule overlay

Make visible the reference and the moving molecules. From the menu item next to the BBB molecule name (right panel), select:

A -> align -> to molecule (*/CA) -> Object: AAA

Antibody's variable domain overlay

I think it may be more helpful to align the variable domains than the whole antibodies or Fabs. Typing the following on the command line is a temporarily adequate way to align proteins:

align BBB and chain A+B and res 1:109, AAA and chain A+BL and res 1:109

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