[Chimera-users] Dock PDB into low resolution EM map.

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jun 12 15:14:03 PDT 2006

Hi Puey,

  Chimera just allows hand placement and local computational position
optimization of atomic models in EM maps.  It does not do any global search
for the best location in the map.

  The hand placement is done by freezing the map so it is not moved by the
mouse.  Do this using the Model Panel dialog (menu Favorites / Model Panel)
and click off the switch in the second column (with heading "Active") to
lock the map position.  Then move the atomic model with the mouse.
It usually requires locking and unlocking the map many times to view
the hand positioning from different angles.  Mesh display or transparent
surface display for the density map is useful.

  Once you get the position approximately right you can do a computational
position optimization that rotates and translates the atomic model so that
the sum of the density values at the atom positions (interpolated map values)
is maximized.  To use this select all atomic model atoms (ctrl-left-mouse click
one atom and press the up arrow key a couple times, or use menu Select / 
Select All (assuming just one atomic model is open).  Then use menu entry
"Tools / Volume Data / Fit Models in Maps" and press the Fit button.  It 
typically takes about 10 seconds then moves the atomic model to the locally
optimal position.  You can undo the motion using menu entry Tools /
Movement / Undo Move.  The goodness of fit is reported as the average density
value at the positions of the selected atoms.  Those values appear in the
Fit dialog status line and also the Reply Log (menu Favorites / Reply Log).


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