[Chimera-users] first time use of chimera

Thomas Goddard goddard at cgl.ucsf.edu
Mon Sep 18 11:25:07 PDT 2006

Hi Rich,

  Here are brief instructions to display a PDB and electron density
map in Chimera and align them.

  Download Chimera 1.2255 from the Snapshot section of the download page


and run the installer.

  Open the PDB and map using Chimera menu entry File / Open....  If you
do this with a PDB file from the Protein Data Bank (www.pdb.org) and an
electron density map from the Electron Density Server (eds.bmc.uu.se/eds)
then they will be displayed aligned.

  Click on the "Mesh" button on the volume dialog that was displayed when
the map was opened.  This allows you to see through the mesh.

  Adjust the contouring level by dragging the vertical bar on the histogram
shown in the volume dialog.

  Use menu entry "Actions / Atoms&Bonds / Stick" to fatten the displayed
molecule so it is more visible.

  Use menu entry "Actions / Color / Red" to make the molecule more visible.

  To show only the density near the molecular model use the "Features / Zone"
menu entry on the volume dialog (Chimera 1.2255 or newer).  Then select all
the atoms with menu entry "Select / Select all" on the main Chimera window.
Then press the "Zone" button at the bottom of the volume dialog.  This
restricts the mesh display to only points within 2 Angstroms of the selected

  If the model does not fit in the map you can move it (rigidly) with the
mouse.  Use menu entry "Favorites / Model Panel".  Switch off the checkbutton
next to the map in the column with heading "active".  This freezes the map
so it is not moved when you use the mouse.  Now rotate and translate the
PDB model by dragging with the left and middle mouse buttons.  To shift the
model into or out of the screen hold the ctrl key while dragging with the
middle mouse button.

  If you get the model close to the right position in the map you can
locally optimize its position using the "Fit models in maps" tool, menu
entry "Tools / Volume data / Fit models in maps".  Select the atoms
(menu "Actions / Select all") and press the Fit button on the fitting
dialog and the PDB model will be moved to the optimal local position.

  If you need to change the molecule conformation or reorient residues
there are other tools that I will describe if you need them.

  Here is more info about map display in Chimera.


More detailed Chimera documentation is in the User's Guide.



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