[Chimera-users] marker coordinates

[Elaine Meng]

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?
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#atombox 
 >

Another possibility is to use Features... Zone to get everything  
within some distance of your markers (not necessarily a rectangular  
box):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#zone 
 >

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).
Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



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