[Chimera-users] Display of a vector in Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 7 09:55:50 PDT 2009

Hi Chuck,
I'm not sure if this is exactly what you mean, but the new command (in  
daily builds only, not version 1.3) "measure rotation" reports the  
transformation of one model relative to another and can create a rod  
that shows the axis of rotation.

Alternatively, you can create arbitrary shapes with specified  
coordinates (including rods, arrows, etc.) in the BILD format and then  
read in that BILD file.  That requires already knowing what  
coordinates you want the shape(s) to have.

And a final alternative, if you just want lines or sticks that connect  
existing atoms, you can create them as "pseudobonds" using a simple  
input format read in by the PseudoBond Reader tool.

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 Jul 7, 2009, at 9:04 AM, Charles Letner, Ph.D. wrote:

> Hello,
> Is there a way to display a vector between two sets of coordinates  
> in Chimera? If the approach is to write a python, any chance I could  
> get a nudge in the right direction on chimera commands to work  
> with?  I've written a minimal amount of python code but not related  
> to Chimera.
> Cheers,
> Chuck

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