[Chimera-users] Display axes for global frame of reference?

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 7 10:49:55 PDT 2007

Hi Andy,
It is easy to write out the transformed coordinates of a PDB file.  If 
you have just one model open, the "Save PDB" dialog (for example, 
opened with File... Save PDB) has a checkbox option "Use untransformed 
coordinates" that you can just uncheck before saving the file.  If more 
than one model is open, saving the transformed coordinates is the 
default (but there is an option you can turn on to save the coordinates 
relative to the untransformed coordinates of another model or of itself 
= its untransformed coordinates).

There is no built-in feature to display the coordinate axes, but here 
(file attached below) is a BILD-format object you can open in Chimera 
to show the axes (X red, Y yellow, Z blue).  Should be named with the 
suffix .bild to be recognized automatically.

The BILD text file is very small and simple.  You can edit the colors, 
scale, offset etc. as desired.  The format is described here:

You might be able to do what you want even without a visual 
representation of the axes, using the "align" command and then rotating 
90 degrees around various axes with "turn"

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

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On Sep 7, 2007, at 9:46 AM, Andrew D. Fant wrote:

> Hello All,
>     I'm considering using Chimera as my general purpose modeling
> graphics front-end and have run into a snag.  I have a protein that I
> need to globally translate and rotate to move several residues to be
> oriented along the x, y, and z axes.  In InsightII, there is an option
> to display the global coordinate system in the main graphics window, so
> that it's easy to manipulate a structure to a given orientation.
>     Is there a way to display the global axes like that in Chimera, and
> is it possible to write out the transformed coordinates of a PDB file
> without a lot of difficulty?
> Thanks,
>       Andy

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