<p>Hi,</p>

<p>I&#39; working on the protein (cytochrome oxidase), that is a complex of 3 to 13 chains. There is a very good model 3D model. The first subunit is quite big and has few transmembrane domains. I would like to choose one amino acid and check which other amino acids are close to my chosen one (there is an interaction between them). Which software could show that?</p>

<p>Thanks,</p>

Pymol can do it, as can Chimera or VMD or other visualization program. You can also script it if visualization is not necessary. [In Pymol, you load your structure and use the "around" or "within" selectors][1].

For example, to select residues within 5Å of histidine 34 you would write the following:

    select my_selection, byres( resi 34 around 5 )

 [1]: http://www.pymolwiki.org/index.php/Selection_Algebra