Rolf Huehne wrote: >Bob Hanson wrote: > > >>Rolf Huehne wrote: >> >> >> >>>Bob Hanson wrote: >>> >>> >>> >>> >>>>OK, well, then, since they messed up there, I highly recommend you use >>>>"connect" just after loading. I've added the test for between-model >>>>bonding in Jmol 11.3.48 >>>> >>>> >>>> >>>> >>>> >>>I don't fully trust the connect mechanism in Jmol (I saw for example >>>hydrogen atoms bonded covalently with 2 other atoms in close proximity >>>[a single model file]). Therefore I would prefer to display the >>>"official" bonds. >>> >>> >>> >>> >>> >>specific example, please? It's true, that if two atoms are very close >>Jmol doesn't apply valence rules to only bond H to one of them. After >>all, there are plenty of situations where H is bonded to 2 atoms >>(boranes, for example). >> >> >> > >Sorry, I don't remember the ID. I noticed it while investigating the >"Chemical Component Dictionary" of the wwPDB and it will be difficult to >find it again within about 7000 structures. Since I have to use bonding >information from the dictionary in order to be able to color the bond >types individually I didn't pay much attention to it. >But as far as I remember it were plain C-H bonds and one of the carbons >had five bonds because of this. And the dictionary also showed different >bonds. (The distance of the hydrogen to the carbons was nearly identical.) > > > Well, it would be good to find that. Something almost certainly was odd about the positions of the H atoms in that file.
>Regards, >Rolf > >------------------------------------------------------------------------- >SF.Net email is sponsored by: The Future of Linux Business White Paper >from Novell. From the desktop to the data center, Linux is going >mainstream. Let it simplify your IT future. >http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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 ------------------------------------------------------------------------- SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users