Hi all, RIght now, if you do "Actions->Atom/Bonds->backbone only" Chimera shows the minimum number of atoms to produce a connected peptide/ nucleic acid backbone, which therefore does not include peptide carbonyl oxygens nor nucleic sugar rings/charged phosphate oxygens. We are thinking of changing the behavior so that "backbone only" includes everything that isn't in the side chain/base. The question is: does anyone need/want the current behavior? If not, I'd not only change "backbone only" but would also change Select->Structure-
backbone from a menu (has "full" and "minimal" in it) to just a menu item that selects the full backbone. If there are some people who do use the current behavior, then instead I'd change "backbone only" to be a menu too.
--Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
On Thu, 11 May 2006, Eric Pettersen wrote:
Hi all, RIght now, if you do "Actions->Atom/Bonds->backbone only" Chimera shows the minimum number of atoms to produce a connected peptide/ nucleic acid backbone, which therefore does not include peptide carbonyl oxygens nor nucleic sugar rings/charged phosphate oxygens. We are thinking of changing the behavior so that "backbone only" includes everything that isn't in the side chain/base. The question is: does anyone need/want the current behavior? If not, I'd not only change "backbone only" but would also change Select->Structure-
backbone from a menu (has "full" and "minimal" in it) to just a menu item that selects the full backbone. If there are some people who do use the current behavior, then instead I'd change "backbone only" to be a menu too.
--Eric
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
It is a nice feature to have a quick button to grab just C,CA,N atoms. Although, one could make the argument that a short Chimera script would work just as well or better for customization. I am thinking of teaching new students about molecular graphics and not sure if I'd like to lose the backbone minus CO oxygen option. Eric ______________________________________________________________________ Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University Nashville, TN 37232-8755 Tel: (615)-936-5579 (MRB III) Tel: (615)-322-3303 (5119 SC) Fax: (615)-936-2211 "All that is gold does not glitter, not all those who wander are lost." J.R.R. Tolkien - Fellowship of the Ring
A reasonable number of people have a preference for the current behavior, so we'll offer both as options. --Eric On May 11, 2006, at 2:59 PM, Eric Pettersen wrote:
Hi all, RIght now, if you do "Actions->Atom/Bonds->backbone only" Chimera shows the minimum number of atoms to produce a connected peptide/ nucleic acid backbone, which therefore does not include peptide carbonyl oxygens nor nucleic sugar rings/charged phosphate oxygens. We are thinking of changing the behavior so that "backbone only" includes everything that isn't in the side chain/ base. The question is: does anyone need/want the current behavior? If not, I'd not only change "backbone only" but would also change Select->Structure->backbone from a menu (has "full" and "minimal" in it) to just a menu item that selects the full backbone. If there are some people who do use the current behavior, then instead I'd change "backbone only" to be a menu too.
--Eric
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
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Eric Pettersen