[Chimera-users] Counting atoms within density map contour

Tom Goddard goddard at cgl.ucsf.edu
Fri Mar 23 13:25:53 PDT 2007

Hi Gary,

  You asked yesterday whether it is possible to count the atoms lying 
outside the contour surface of a EM map after fitting.  This can be done 
although it currently requires a few steps.  Here's how.

  1) fit the atomic model into the map as desired.
  2) Use menu entry Tools / Volume Data / Values at Atom Positions, 
choose the molecule and map and press the Histogram button.  This shows 
a histogram of the map values interpolated at the atom positions.
  3) Press the "Select" tab on the Render / Select by Attribute dialog 
and choose Attribute "value_mymap.xxx", move the rightmost green bar on 
the histogram to match the contour level, then press the Apply button.

This procedure selects the atoms at lower density levels than the map 
contour level and you can see the number of atoms selected in the lower 
right corner of the main graphics window.  You can press the up arrow 
key a few times to select all atoms in the molecule to see the total 
number of atoms.

  I show a picture below fitting 1i84.pdb into myosin.map where 2727 of 
16070 atoms lie outside the contour surface.  I colored the selected 
atoms outside the contour blue in the picture.


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