It seems that this thread got lost. I did send Bob a test file; will send it again now.
11.6.RC13_dev still draws type 4 bonds (aromatic) as alternating double- single. I don't like that. Type 8 are dotted or partial, which I suspect the behavior with 4 may be intentional, is it so? And how can I make them look aromatic? (maybe with the aromatic command? or was it calculate? I never catched it) On 17 Jul 2008 at 0:25, Bob Hanson wrote: > I'll need some specific file examples, please. > > Angel Herráez wrote: > > >According to a previous report of mine (which went into doc. in the Wiki) > >http://www.mail-archive.com/[EMAIL PROTECTED]/msg09232.html > >in MOL format files, bond type 8 (described as "any") used to be interpreted > >by Jmol as > >partial bond. Now I see it is not so; bond is not drawn. > > > >I'd like to know if this is intended, or I was wrong, or it is a bug in > >recent versions. > >11.5.46 and 11.4.5 do not draw any bonds for type 8 > >11.3.11 draws them as partially double, or no bond, depending on the atom or > >its > >neighbors?. > > > >I understand that since MDL doc does not assign "partial" meaning to type 8, > >if may be more > >sensible for Jmol not to interpret as so. However, no bond at all where a > >bond is specified is > >not a faithful solution either. > > > >While I am at it, I also see that type 4 (aromatic) is rendered as partially > >double by 11.3.11 > >but as alternating single and double bonds by 11.4.5. I guess that's a > >conscious > >consequence of the recent "aromatic" and "calculate aromatic" commands, > >right? > >I'd rather prefer that the aromatic-specified bonds are drawn as partially > >double, but I won't > >push for it. Just want to mention is case it is an inadvertent change. > > > >Well, there's even more. Here's a summary across versions: > > > >bond type 4 > >11.3.11: aromatic (partially double) > >11.4.5: alernating single and double bonds > >11.5.46dev (8 july 08): aromatic (partially double) > > > >bond type 8 > >11.3.11: partially double !! > >11.4.5: no bond > >11.5.46dev (8 july 08): no bond in some cases, double in others!! > > > >I also note that in 11.5.46, some single bonds are drawn as double > > > > > > > > > >------------------------------------------------------------------------- > >Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! > >Studies have shown that voting for your favorite open source project, > >along with a healthy diet, reduces your potential for chronic lameness > >and boredom. Vote Now at http://www.sourceforge.net/community/cca08 > >_______________________________________________ > >Jmol-developers mailing list > >[email protected] > >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
