Second conformation validity.

Leonard Pattenden ddlpatte at mailbox.uq.edu.au
Mon Nov 30 21:29:24 EST 1998


G'day all;

I'm building a second conformation for a side-chain in O, however to get
the side-chain properly into the density I have to radically alter the Psi
and Phi options in tor residue. The altered Psi and Phi geometries allows
nice fitting to the density of the side chain from Cb onwards (residue is 
a Glu located near the protein surface, the resolution is 1.6A).

My question: 

Is it considered "valid" to set a second conformation in this way.
Especially if you consider the first conformation will contain the C-alpha
trace of the main-chain and not the altered Psi and Phi geometries, with
the second conformation being Cb onwards only. I probably wouldn't
consider the second conformation main-chain as valid as it looks a bit
radical for the pretty definitive density. I cannot see the side-chain
easily "flipping" or "swaying" (as a natural motion of surface residue) 
into the position I have constructed for the second conformation. I am
curious as to peoples views on the validity of such a change.

Have a day!
                            \\|//
Len...                     \`_ _'/   
                           ( @ @ )
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              "Life is a comedy for the thinking man,
               Life is a tragedy for the feeling man."

                                  William Shakespeare
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                          \_)    ) /  3D Centre for Drug Design &
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