Label all atoms except hydrogens
How would I label all atoms in a structure without labeling hydrogen atoms? I'm trying to label a small molecule with about 60 non-hydrogen atoms. Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <<< ------------------------------------------------------------------------>>>
Hi Mike, There are several possible routes to achieving this, but a concise one is the command: label ~ element.H where the "~" is a logical NOT. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combina...> Or, you could label all atoms and then unlabel hydrogens, or do the menu equivalents of either of those routes. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 21, 2010, at 1:59 PM, Michael Day wrote:
How would I label all atoms in a structure without labeling hydrogen atoms? I'm trying to label a small molecule with about 60 non-hydrogen atoms.
For future ref, even more concise: label ~H maybe you already knew that and just wanted to use something more self explanatory -- if so, I never sent this! --E On Oct 21, 2010, at 2:14 PM, Elaine Meng wrote:
Hi Mike, There are several possible routes to achieving this, but a concise one is the command:
label ~ element.H
where the "~" is a logical NOT. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combina...
Or, you could label all atoms and then unlabel hydrogens, or do the menu equivalents of either of those routes.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2010, at 1:59 PM, Michael Day wrote:
How would I label all atoms in a structure without labeling hydrogen atoms? I'm trying to label a small molecule with about 60 non-hydrogen atoms.
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I hate Reply-To headers! --Eric On Oct 21, 2010, at 2:28 PM, Eric Pettersen wrote:
For future ref, even more concise: label ~H
maybe you already knew that and just wanted to use something more self explanatory -- if so, I never sent this!
--E
On Oct 21, 2010, at 2:14 PM, Elaine Meng wrote:
Hi Mike, There are several possible routes to achieving this, but a concise one is the command:
label ~ element.H
where the "~" is a logical NOT. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combina...
Or, you could label all atoms and then unlabel hydrogens, or do the menu equivalents of either of those routes.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2010, at 1:59 PM, Michael Day wrote:
How would I label all atoms in a structure without labeling hydrogen atoms? I'm trying to label a small molecule with about 60 non-hydrogen atoms.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine and Eric, Thanks. Works great. I don't see the menu options but that's okay as I'm fairly comfortable with the command line anyway. P.S. don't get the reply-to header comment. Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <<< ------------------------------------------------------------------------>>> On Oct 21, 2010, at 2:14 PM, Elaine Meng wrote: Hi Mike, There are several possible routes to achieving this, but a concise one is the command: label ~ element.H where the "~" is a logical NOT. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combina...> Or, you could label all atoms and then unlabel hydrogens, or do the menu equivalents of either of those routes. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 21, 2010, at 1:59 PM, Michael Day wrote:
How would I label all atoms in a structure without labeling hydrogen atoms? I'm trying to label a small molecule with about 60 non-hydrogen atoms.
Hi Mike, The menu approaches would involve some selection steps and then applying the action, e.g. Select... Chemistry... element... H Select... Invert (all models) Actions.. Label... name Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 21, 2010, at 3:55 PM, Michael Day wrote:
Elaine and Eric, Thanks. Works great. I don't see the menu options but that's okay as I'm fairly comfortable with the command line anyway. P.S. don't get the reply-to header comment.
(Eric had meant to reply to just me, but I'd set the "reply-to" field to the whole list, thus the whole list got to see it)
participants (3)
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Elaine Meng -
Eric Pettersen -
Michael Day