[Chimera-users] Can eraser position be defined by coordinates?

Tom Goddard goddard at sonic.net
Mon May 16 12:18:01 PDT 2011

Hi Kelly,

   There is no command to position the volume eraser sphere using typed 

   If you want to erase a spherical region centered on the center of a 
virus map use the shape and mask commands:

     shape sphere radius 120 center 0,0,0 coord #0 color blue
     mask #0 #1 invert true

The first command makes a spherical surface of radius 120 Angstroms at 
center 0,0,0 (Angstroms) in the map #0 coordinate frame colored blue.  
The second command copies the region of map #0 outside the sphere #1, 
making a new volume data set.

   The main trouble here is figuring out the coordinates of the center 
of virus map.  The virus map origin is set in the Volume dialog 
Coordinates panel where you specify the grid index for position 
(0,0,0).  In the above example I've got the map origin set to the center 
of the virus (EMDB 1058, grid index 87 for a size 175 map, base index is 
0).  You can use

         shape sphere radius 120 center #0 color blue

which puts the center at the center of the bounding box of the displayed 
surface for map #0.  But that doesn't in general give you the exact 
center of symmetry.  So it is better to find the exact grid point that 
is the center of symmetry used when the map was calculated.


> Hi,
> I would like to place the origin of the eraser to correspond with the
> center of my map but haven't found a way to define its position based on
> coordinates, only by moving it with the mouse.  Is there a line command
> or other menu option that allows me to set the position more precisely?
> Thanks,
> Kelly
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> Chimera-users at cgl.ucsf.edu
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