Defining a zone around a point defined by x, y, z coordinates
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@uab.es
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@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@uab.es
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. --Eric 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@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@uab.es
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
Jean-Didier Marechal