[Chimera-users] coordinates

Tom Goddard goddard at cgl.ucsf.edu
Fri Jan 25 10:35:03 PST 2008

Hi Hernando,

  A map in Chimera has a coordinate system where the x,y,z position of 
the data value at grid index 0,0,0 can be anywhere, and the spacing 
between grid planes along the 3 grid axes can be any distance.  Those 
parameters for a given volume are shown in the Coordinates panel of the 
Chimera volume dialog (1.2470 and newer).  The values come from the map 
file header.  They can be changed and you can save a new map if 
desired.  In general an atom placed at x,y,z = (0,0,0) will not be at 
the middle of a map.

  A PDB file has an xyz coordinate system and the atom coordinates are 
given in the PDB file.  If you open a map and a PDB model then their xyz 
coordinate systems are the same.  But if you freeze the map (for 
example, with the "active" button on the model panel) and move the PDB 
model, then the coordinate systems of the PDB and map no longer match 
up.  There is a rotation and translation relating the two coordinate 
systems that Chimera remembers.  This is where saving the PDB relative 
to the map is handy.  The PDB atom positions get written out using the 
coordinate system of the map with that setting, instead of relative to 
the molecule's coordinate system.

  I don't know how you are rotating the the molecule.  Most methods 
(e.g. movement with mouse) use a center of rotation that is not xyz = 
(0,0,0) since that may be far off the screen.  Usually Chimera uses the 
center of the bounding box of the displayed molecules and maps as a 
rotation center.  Another choice is to have the rotation center fixed in 
the middle of the screen and midway between clip planes in depth.  Or it 
can be fixed at specific coordinates.  The current setting is shown 
using menu entry Tools / Movement / Rotation.

  Hope this clarifies some of the coordinate system workings.


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