From: Jairav D. <jairavdesai2008@u.northwestern.edu> - 2009-04-06 18:40:34
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I just want to confirm, so if I use the pdb format, I don't need to specify these xyz coordinates? i can just specify the bonds? 2009/4/6 Robert Hanson <ha...@st...> > yes, that should work like a charm. Have fun with this! > > > > On Mon, Apr 6, 2009 at 12:02 PM, Jairav Desai < > jairavdesai2008@u.northwestern.edu> wrote: > >> Thanks for the reply. I will try it out with phosphorus atoms. >> if you take a look at this image >> http://www.umassmed.edu/faculty/graphics/182/DekkerFig2new.gif >> >> In the way you see above, I'm trying to find a simple way to make a >> straight line (which represents the gene) and pull together the interacting >> regions without having to describe all the x,y,z coordinates because all >> that I need is to be able to define the two regions which are close by (like >> in the image) assuming that all the consecutively listed regions are bonded >> together. >> >> jairav >> >> 2009/4/4 Angel Herráez <ang...@ua...> >> >>> 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 >>> >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > High Quality Requirements in a Collaborative Environment. > Download a free trial of Rational Requirements Composer Now! > http://p.sf.net/sfu/www-ibm-com > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |