I have binding site of two homologous crystallographic structures.


PDB_01 contains 24 amino acids:

Leu44, Gly45, Phe49, Val52, Ala65, Lys67, Glu89, Ile104, Leu120, Glu121, Arg122, Pro123, Val126, Asp128, Asp131, Glu171, Asn172, Leu174, Ile185, Asp186, Tyr215, Arg274, Pro275, Ser276.


PDB_02 contains 18 amino acids:

Leu44, Gly145, Phe49, Val52, Ala65, Lys67, Glu89, Ile104, Leu120, Glu121, Arg122, Pro123, Val126, Asp128, Asp131, Leu174, Ile185, Asp186.


I used “fit” command to calculate rms.

fit PDB_01, PDB_02

Executive: RMS = 0.706 (143 to 143 atoms)


I have two questions


  1. To my knowledge “fit” command works only if there are equal number of amino acids between the structures. If so, then how “fit” worked with 24 vs 18 amino acids?

  2. I want to calculate rms for all the atoms (i.e., including side chain atoms) between these two structures. Among “fit” and “align” command, which will be the best option?


I cant understand very well from “help fit” or “help align”. Can anyone explain me?

Thanks in advance!!!

Renuka.