Renuka,

In this case the 'fit' command is detecting the residues that are common between your two sequences and fitting those.  The operator in question here is "in".  You can select atoms from one chain that are "in" another.  For example,

# load your two proteins p and q, then select the
# residues from p that are in q:

select p_pocket in q_pocket

Let's check and see if that's what fit is doing in your case:

# what you typed

fit p_pocket, q_pocket


# fitting manually against just those residues from p in q,
# and from q in p

fit p_pocket in q_pocket, q_pocket in p_pocket

You get the same answer.

Last, to get a list of the residues fit uses, just issue the first select command above.

Cheers,

-- Jason


On Wed, Apr 21, 2010 at 11:49 AM, Renuka Robert <renukarobert@ymail.com> wrote:

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.



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