2011/9/14 Angel Herráez <[email protected]> > > Does Resolver output a 2D or 3D tag in those columns? > > > > It does it properly, and Jmol reads that tag. It's just that we don't > > process the file as 2D (with minimization) unless you specifically > > request that. > > Ah, that's new to me. I had written the oppsite in the Wiki. > So is there a difference in action by Jmol depending on whether the > tag reads 2D or 3D? For a plain load, or for a load filter "2D"? > > Specifically for the V3000 format, Jmol will read the 2D tag and automatically equate that with FILTER "2D" but only for V3000. Not V2000 or the older MOL file formats.
That's not exactly consistent, I know, but the idea was for MOL/V2000 files to at least still retain the option to read them as is. > > > Realize that just because the file is 2D doesn't mean Jmol should > > modify it. That's the issue. > > OK, you are right, that's sensible. > > > I'm testing 'load data ... filter "2D" ' and it's working fine, > except I still seem to have problem with trisubstituted carbons -- > like trimethylmethane-- the central carbon does not get its hydrogen > (sample file attached) > > load "isobutane_2D.mol" filter "2D"; > > Quite possible. It's only approximate. Why the need to do this with 2D files? -- 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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