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
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?
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.
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