[Chimera-users] loading atomic coordinates without drawing or calculating bonds

Eric Pettersen pett at cgl.ucsf.edu
Wed Aug 5 09:58:56 PDT 2009

On Aug 5, 2009, at 2:52 AM, Veysel Berk wrote:

> Hello,
> I am trying to load a large atomic coordinates file in xyz format.  
> The atomic coordinates are meaningless to crystallography in terms  
> of distances of atoms and as a result, while chimera try to load the  
> coordinate and calculate the bonding between atoms, it crashes or  
> suspends for ever. The data is from single molecule localization  
> experiments where I want to use chimera to visualize this 3D data by  
> treating each localization as an atom. I am trying to load about a  
> million atoms.
> Is it possible to turn off automatic bonding calculations and only  
> show atoms without bonds to prevent crashing? or does anyone know  
> any simple method or software to convert atomic coordinates into  
> voxel map which I can use in volume visualizer module of chimera  
> without worrying about bond calculations?

Hi Veysel,
	I don't know if there's a particular reason you want these points to  
be atoms, but one alternative is the use the ".sphere" directive of  
Chimera's BILD format (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html 
) to depict your points.
	If you do need them to be atoms, there is no way to suppress the  
connectivity search for XYZ files without editing the Python code for  
reading that file format.  If you are willing to do that then the  
change is pretty trivial.  In the __init__.py file of the ReadXYZ  
module there is a line that looks like this:


either delete that line or insert a '#' symbol just in front of the  
'c' to comment it out.  You will find ReadXYZ in the 'share'  
subdirectory of your Chimera installation.  On a mac it will actually  
be in the 'Contents/Resources/share' subdirectory and you will have to  
right click on the Chimera icon and choose "Show Package Contents" to  
see the application subdirectories in the Finder.
	I hope this helps.


	Eric Pettersen
	UCSF Computer Graphics Lab

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