[Chimera-users] questions using chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 12 15:46:09 PDT 2007

Hi Xiaoyun,
(1) There is no function to display the axes currently, but I  
attached at the bottom of this message a BILD object file showing the  
X,Y,Z axes in red, yellow, and blue.  BILD is a very simple text  
format, and simply opening the file in Chimera shows the object.  The  
drawback is that the position and scale of this object are not  
automatically adjusted depending on what you have displayed.  You  
could change its origin by editing the coordinates in the  
".translate" line and its scale by editing the number in the ".scale"  
line.  Format description:

(2) Funny you should ask, but we just added a "top view" option to  
the Side View.  It is available in the most recent snapshots (dated  
Apr 11 for Windows and Linux, Mar 26 for OSX although the GUI text  
was a little different then).  You can switch between the two views.   
The top view shows the XZ plane with Z pointing left, toward the  
viewer. Here is a picture and description:

snapshot download:

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 12, 2007, at 11:29 AM, Xiaoyun Chen wrote:

> I have two questions:
> 1) Is there a way for chimera to display the x-y-z axes? For example,
> for a pdb file, all the x/y/z coordinates are referenced to the
> molecular coordinate system. In the chimera screen, we can rotate the
> molecules. I want to know the orientation of the molecular coordinate
> system in the laboratory/chimera coordinate system, but cannot find a
> way for the x/y/z to show up on the screen. Many other protein
> visualization software (VMD, Molw, etc) have this feature.
> 2) by default, the z coordinate point out from the screen. often i
> would like to see the protein with its z direction in the plane of the
> screen and pointing up. tools-viewing controls-side view allow me to
> get what i want, but the image is only the protein projected onto the
> y-z plane. but it would be nice if there are two side view panels, one
> with an image in the y-z plane, one with an image in the x-z plane.
> Thank you!
> Xiaoyun Chen

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