From: Robert H. <ha...@st...> - 2009-04-08 13:16:37
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Good point, Angel. set autobond off will be important. It needs to come before the file loads, otherwise Jmol will attempt to make bonds based on bond distance. Bob 2009/4/7 Angel Herráez <ang...@ua...> > On 6 Apr 2009 at 13:40, Jairav Desai wrote: > > > > > 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? > > No. You need xyz coordinates always; there is no way the atoms can be > positioned without coordinates. > And pdb format does not (usually) specify bonds. The idea is that by > assigning a correlative residue number to each atom, Jmol will join them in > sequence when you use "trace" or "ribbon" > > Example: > REMARK Dummy model; each atom is a residue in a nucleic acid chain > ATOM 1 P UNK 1 1.6 0.0 0.0 > ATOM 2 P UNK 2 9.5 0.0 0.0 > ATOM 3 P UNK 3 2.3 -1.5 2.0 > ATOM 4 P UNK 4 -2.2 -1.5 -1.0 > ATOM 5 P UNK 5 -4.0 -2.1 2.5 > ATOM 6 P UNK 6 1.7 -0.5 2.7 > END > > Then, type these commands: > set autobond off > trace 0.25 > > Note: distances among the atoms must not be too long, or the trace will not > be drawn. > > > > > ------------------------------------------------------------------------------ > 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 > -- 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 |