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.) 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
