[Important question for Eric Martz.] 2010/1/10 Angel Herráez <angel.herr...@uah.es>
> > 3) keep the oldest OpenBabel 1.0 set as JMOL > > If this keyword is totally new, I'd propose to call it something like > CLASSIC. Since JMOL will > not be the default option, its name may be misleading. > > The current default is "Jmol", so we would need to recognize that still. But we could change it to "BABEL11" if desired. > > > > 4) add a "set DEFAULTVDW AUTO" option (which would be the default > behavior), which > > preserves the JMOL default for traditional PDB files having no H atoms > but switches to BABEL > > when hydrogen atoms are present or when the file doesn't have residues. > > I don't like the idea of having different results with different models > under the same "set" > option --more so being the default. Maybe keeping the previous aspect for > nonH PDB > models is important, but most users won't notice. I'd rather go for a > "BABEL for all" solution. > That would be a big move. We'd need to see what Eric Martz and company think, since that would definitely change the molecular surface visualization for traditional PDB files. (It would, of course, CORRECT the visualizations for H-containing PDB files, but I think that's a small subset of what is out there.) One question is: What do programs such as Pymol or VMD do? Do they first add hydrogens and then do a Babel-type VDW -based surface? Can someone check on this? Eric? > > > > 5) make the default VDW radii model-dependent, so if you open caffeine > and 1CRN.PDB and > > 1CDR.PDB all will look correct. Caffeine and 1CDR will both load using > the BABEL set; 1CRN > > will load using the JMOL set. > > This again makes me uncomfortable, even more than the previous item. Having > atoms > change size depending on which model they belong sounds frightening ;-). > It would only kick in if the the model is clearly a PDB file and has no hydrogen atoms. -- 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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