[Chimera-users] marker coordinates

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 26 09:58:01 PST 2009

Hi Gabor,
I am pretty sure the capabilities are still there, but maybe the  
dialog has been rearranged -

In the Volume Viewer dialog, choose Features... Atom box - is that  
what you had in mind?

Another possibility is to use Features... Zone to get everything  
within some distance of your markers (not necessarily a rectangular  

For both of those, you would first need to select all the markers of  
interest.  To get the (untransformed) coordinates of the markers, you  
could save them to a file from the Volume Tracer tool, or select them  
and use the command:

getcrd sel

which sends the coordinates to the Reply Log (under Favorites).
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 26, 2009, at 4:43 AM, Gabor Papai wrote:

> Hi,
> I would like to do the following: I placed markers on density spots. I
> want to get their coordinates and excise a box around the marked  
> density
> and save it as a separate file. For this I would like to know how I  
> can
> retrieve the coordinates of a marker set and possibly how to position
> exactly a box around a  marker to set a subregion (and of course how  
> to
> set the dimensions of that box). This second feature existed before,  
> but
> disappeared in the latest releases with the subregion selection tool  
> in
> the Volume Viewer.
> Thanks in advance,
> Gabor

More information about the Chimera-users mailing list