[Chimera-users] coordinates

hsosa at aecom.yu.edu hsosa at aecom.yu.edu
Fri Jan 25 12:20:24 PST 2008


I am trying to use the sym command to generate symmetric molecules in a 
helical  map.  I have done the following

1 ) Put the molecule in the right place in the map.
2) Save a new pdb file of the molecule with coordinates relative to the 
map. (I reopened the map and the new pdb file and checked that they were 
at the chosen locations relative to each other).
3) Write with a text editor  the helical symmetry operations for two 
molecules in the header of the recently created pdb file (rotation 
around the Z axis and translation along the Z axis).
4) Open in chimera the map and pdb file with symmetry header.
5) Use the sym command to generate the two symmetry related molecules.

Result: The two extra symmetry related molecules appear, but the center 
of rotation seem to be around the bounding box corner instead of being 
around the axis of the map which is located in the middle of the 
bounding box.

The map that I am using  is in  the XY dimensions 151 by 151 pixels with 
a voxel size of 4A. The helical axis is parallel to the Z direction and 
crossing the center of  the box.  I have tried the above procedure by 
either first setting the origin of the map at 0 0 0 or at  300 300 0 (so 
that the axis of the helical map will  cross the center of the XY plane) 
but still  I don't seem to get it right. I'm not sure what I am doing wrong.

One thing that I tried and worked was to:
1) Open the map, set voxel size to 4 and origin to 300 300 0.
2) Open molecule pdb file and move it to the right location in the map.
3)  Save a new pdb file with the coordinates relative to the map.
4) Create a new pdb file with a utility of my own that apply the symetry 
operations (rotation & translation). In this case I located the axis of 
rotation parallel to the Z axis and at  x = 300  y = 300 (the XY center 
of the 3dmap in Angstroms).

The resulting pdb file does have the three molecules at the exped 
locations relative to the map. However it would be more convenient for 
fitting purposes to do it using the sym command instead of generating a 
new pdb file with the coordinates of all the symmetry related molecules.


Tom Goddard wrote:
> 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.
>    Tom

Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu

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