[Chimera-users] Geometric Center

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 15 11:31:06 PST 2016

Hi Tobias,
Basically you would first calculate the center of the set of atoms, then subtract its coordinates by translating along X,Y,Z, and then saving the transformed coordinates.

For calculating the center, you can do mass-weighting or not, and you can specify exactly which set of atoms you want, using the same Chimera “atomspec” syntax as in other commands.  For example, commands like:

define centroid mass false <atoms>
define centroid mass true <atoms>
measure center <atoms>

… where the latter does mass weighting and <atoms> can be any Chimera atomspec such as: 
 (all atoms of model 1, which would include any solvent, ions, ligands ...)  
(all protein atoms) 
#1 & protein
(all protein atoms in model 1)


The coordinates of the center will be reported in the Reply Log (open from Favorites menu).  Then, command “reset” will remove any mouse rotations/translations you might have done.  Without moving the structure at all with the mouse, use the “move” command to subtract out the coordinates of the center.  For example, if center is reported as:

centroid name, ID, center: centroid: c3 ( 35.247,  30.064,  49.104)

I would use commands:

move x -35.247
move y -30.064
move z -49.104

then File… Save PDB, uncheck “Use transformed coordinates” since you want the transformed coordinates.  Or, you can save PDB with the “write” command.

I checked by reading the new PDB back in and calculating center again with the same set of atoms.  The coordinates weren’t exactly zero, I guess because of rounding issues, but close: -0.03, -0.01, -0.01).

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 14, 2016, at 11:36 PM, tobias.eilert at uni-ulm.de wrote:

> Hello,
> I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this.
> Do you have any suggestions?
> With kind regards
> Tobias Eilert

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