[Chimera-users] Surfactant

Thomas Goddard goddard at cgl.ucsf.edu
Mon Aug 14 16:13:17 PDT 2006

Hi Annalisa,

  The Chimera Multiscale tool makes a low resolution surface for each
chain of a PDB model.  You could put all of type A surfactant
molecules in one chain, and all type B surfactant molecules in another
chain.  Open the model in Chimera (menu File / Open) then use menu
entry Tools / Higher-Order Structure / Multiscale Models, select
Multimer type "None" at the bottom of the dialog and press the "Make
models" button near the bottom.  You'll probably want a higher surface
resolution than the default 8 angstroms.  Press the Select "All"
button at the top of the multiscale dialog, then change the resolution
value (middle of dialog) from 8 to 3 and press the Resurface button.
By using two PDB chains you will have two surfaces -- one for each type
of surfactant.  Each can be colored by selecting it (hold ctrl and
click on it with mouse button 1), then press the Color button in the
multiscale dialog and choose a new color.

  The multiscale dialog is also able to use matrices to position
copies of molecules as Elaine noted.  But since your surfactant
molecules are all in different conformations I don't think that will
help you.


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