Note also that since you only have ATOM records and occasional END markers, you could just load that file with the load() function and do anything you want with it, including delivering whatever column fields you want to atom properties.
On Tue, Aug 9, 2011 at 10:55 PM, Robert Hanson <[email protected]> wrote: > > > On Tue, Aug 9, 2011 at 3:31 AM, Pascal Auffinger < > [email protected]> wrote: > >> Hi Bob, >> >> Thanks for the advice on using "backbone off". It works fine now. Yet, >> still it is difficult to understand why Jmol connects P atoms separated by >> more than 5 Å in a carbohydrate fine. Anyway, Jmol is pretty robust and it >> can swallow some very unconventional PD files. In fact, we modified pdb >> files in order to be able to tag them with respect to specific criteria. >> Does Jmol read columns that are not defined by the PDB standards like for >> example comments written after the 80 character conventional PDB lines or, >> like Pymol, is it possible to use the empty columns after the B-factors for >> writing symmetry codes (see D0Z0 below). >> >> > Jmol tries to connect backbone atoms if it finds no bonds whatsoever in a > chain. This just looks better than having dots everywhere. In this case, > since you are faking the residue names and giving some the names of known > carbohydrates, Jmol detects that and connects their backbones when they are > adjacent. > > You can put anything you want after the 80 columns. > > > > >> Example of a ymol pdb line containing a symmetry code >> ATOM 1086 N ARG A 51 29.887 -6.322 19.972 1.00 30.33 >> D0Z0 N >> >> Being able to read symmetry codes or comments would be really useful for >> us (if a similar option is not yet available). >> By the way, is there a symmetry marker in Jmol ? >> > > Jmol has full support for PDB symmetry and reads biomolecules correctly, > for example. No need to invent your own. > > > >> >> Pascal >> >> >> >> >> >> ------------------------------------------------------------------------------ >> uberSVN's rich system and user administration capabilities and model >> configuration take the hassle out of deploying and managing Subversion and >> the tools developers use with it. Learn more about uberSVN and get a free >> download at: http://p.sf.net/sfu/wandisco-dev2dev >> >> >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > 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 > -- 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
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