[Chimera-users] force fitting a protein into select volume in a EM reconstruction

Thomas Goddard goddard at cgl.ucsf.edu
Tue Oct 17 17:45:54 PDT 2006

Hi Jayant,

  The Chimera fit optimization tool

	Tools / Volume Data / Fit Models in Maps

rigidly rotates and moves the model to increase the average density
value at the positions of selected atoms.  That is not necessarily
what you want.  Depending on your map it may push your PDB model
towards some high density region even though another position better
matches the shape of the map contour surface to the shape of the
molecule.  We don't have any fitting tool to optimize this shape
matching although maybe we should make one.  I could imagine taking a
molecular surface for the PDB model and trying to position it to best
match the contour surface of the EM map.

  The one choice you can make is which atoms you select for doing the
fit.  If some subdomain of your model fits the map well you could just
select that domain.  The fit will move the whole PDB model to optimize
just the density at the selected atom positions.

  If that does not work, the current fitting tool may not be helpful,
and a hand placement may be the best that can be done.  It is possible
to extract just a portion of the map around your hand placed model.


Then you could use the fit optimization tool just on that saved piece of
the map.  But that very likely is not helpful.  Your PDB model will just
move towards the undesirable position until it hits a boundary where you
cut the map off.

  So I think a hand-fit or using other software (e.g. EMFit or Situs)
is the way to go.

  If you hand place your PDB and then the fit optimization messes it
up you can bring the PDB exactly back to the hand placed position with

	Tools / Movement / Undo Move

In general this undoes your previous model movements (remembering a
history of I think 100 previous positions).  This is so useful that I
put it on the Chimera toolbar using Favorites / Preferences, category
Tools, checking the "On toolbar" button for "Undo Move" and the Save
button on the preferences dialog (so it will be on the toolbar in
future sessions).


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