[Chimera-users] Defining a zone around a point defined by x, y, z coordinates

[Elaine Meng]

Hi JD,
There is currently no direct way to get a zone around an (empty) point  
of space. It could be done with Python, but I would just add a fake  
atom with the desired zone-center coordinates to an input PDB file.  It  
could be in a file by itself or lumped together with the structure you  
are studying.

With commands, you can act on zones without going through a selection.   
For example, if your fake atom was named XX:
   rl @xx z<4.5
(label all residues with any atom within 4.5 angstroms of XX)
   color red @xx za<4.5
(color all atoms within 4.5 angstroms of XX red)

Documentation on specifying zones in the command line:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
atom_spec.html#zones

Of course, you can do it the menu way if you prefer.

Chimera does allow interactive atom creation, as opposed to editing a  
file, but  those approaches don't allow you to type in a set of  
coordinates (Build Structure puts an atom in the center of view,  
whereas Volume Path Tracer creates an atom where you click the screen).
I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


On May 8, 2007, at 7:29 AM, Jean-Didier Marechal wrote:

> Dear all,
>
> We are having difficulties in defining a certain type of selection  
> zones
> in chimera. Our  problem is that we don't want to centre the zone on an
> atom selection but on one point of the space defined by its 3D
> coordinates. Typically we want to give chimera the x,y,z coordinates  
> and
> select all the atoms included in a sphere of 25 angstroms around this
> point.
>
> How can we do so?
>
> Thanks a lot
>
> JD
>
> -- 
> Dr. Jean-Didier Maréchal
> Professor Assistant
> Physical-Chemistry Unit
> Department of Chemistry
> University Autonomous of Barcelona
> 08193 Bellaterra, Spain
> Tel: (+34).93.581.49.36
> Fax: (+34).93.581.29.20
> e-mail: jeandidier.marechal at uab.es
>
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