From: Robert H. <ha...@st...> - 2009-04-06 16:36:15
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Jairav, Yes, that's right -- use the PDB format and designate your "atoms" as either CA or P. In fact, you can even use the element symbol field (columns 78 and 79) to designate an element for coloring purposes if you want independently of whether the atom name is "CA" or "P" Also, then you can use the temperature field as an additional selection or coloring criterion. On Sat, Apr 4, 2009 at 10:30 AM, Angel Herráez <ang...@ua...> wrote: > Hello Jairav > > > The model is meant to be roughly representative, so I just want to > > draw a "ribbon" (or rather noodle view where each DNA base is displayed > by an atom (to > > simplify) > > Yes. It should work if you set the atoms as phosphorus. I think that Jmol > will join them > automatically in ribbon or trace mode (it sure does it for alphaC-only > proteins). > > > > To make this easier on me, I was wondering if there is a file format for > JMOL which uses the > > consecutively numbered atoms and assumes bonds between them, > > Not because the atoms are consecutively numbered. But it will work, as I > said, if you use > pdb format and put residue numbers. > > > > and then places them > > without requiring x,y,z coordinates. > > I see no way how it can work without xyz coordinates. Everything in Jmol is > based on those. > > > > Ideally I'm looking for a way to just put in relative coordinates > (distance geometry file for > > example). > > Can you clarify what you mean by that? > > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |