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

Eric Pettersen pett at cgl.ucsf.edu
Tue May 8 11:57:54 PDT 2007

A minor alternative is to use a single-atom PDB with coordinates at  
(0,0,0) and then, with only it active for movement, use the "move x",  
"move y", and "move z" commands to get it to the coordinates you want  
-- whichever is more convenient for you.


On May 8, 2007, at 11:28 AM, Elaine Meng wrote:

> 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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