[Chimera-users] structure slice

Thomas Goddard goddard at cgl.ucsf.edu
Mon Aug 14 15:56:02 PDT 2006

Hi Raquel,

  The documentation Elaine suggests will help show a slab of your
virus EM map.

  Here are a few specific details.

  Open your map using Chimera menu entry File / Open....  I used
em_1015 from the VIPERdb web site.  Figure out where the 3 fold and
fold axes are.  I used menu entry Tools / Higher-Order Structure /
Icosahedron Surface and displayed the different orientation to find
one that matches the map.  Orient the 3-fold axis perpendicular to the
screen.  The map I tried had 2-fold axes along x, y, and z axes
(orientation xyz 2-fold axes in icosahedron tool).  So I displayed the
Chimera command line with menu entry Favorites / Command Line and
typed command "turn y 20.905157448" This rotates the models about the
screen y axis by 20.9 degrees which is the angular separation between
a 2-fold axis and nearest 3-fold axis.  If you have rotated your model
with the mouse, first put it back to the standard orientation by
typing the command "reset".  Next I used menu Favorites / Side View
and dragged the left vertical yellow line in the side view window into
the particle.  That is the front clip plane.  And I dragged the back
clip plane (right vertical yellow line) into the particle.  Then I
used menu entry Tools / Depiction / Surface Capping and turned on the
switch to "Cap surfaces at clip planes".  This covers the holes left
when clipping the surface.  You can adjust the contour threshold level
by moving the vertical bar on the histogram in the volume dialog which
appeared when you first opened the EM map.  You can precisely control
the thickness of the slab using the Camera tab of the Side View
window, setting the numeric values of the near and far clip plane.
You can color the sliced part of the map according to density value
using menu entry Tools / Volume Data / Surface Color described here.


The side view clip planes I used are always parallel to the screen.
You can use "per-model clip planes" that rotate with the model using
menu entry Tools / Depiction / Per-Model Clipping.

  Alot to figure out.


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