Hello Tian Jmol draws bonds if the distance between the atoms falls within some range of the sum of van der Waals radii for those two elements. Or when the file includes bond information. Or when there is an explicit connect command in JmolScript
> When I open my structure I can always see some bonds break, though they are > supposed to be > bond. Supposed by what rule? Can you share your file for us to look at? > I think there are some parameters to define the threshold in J mol, but I > don't know where are > they, and how to change them...... Yes, I think there is one that controls the threshold. Otherwise, you can specify, create and delete bonds at will using the "connect" command. ... Ah, there you are: set bondTolerance http://chemapps.stolaf.edu/jmol/docs/#setbondstyles ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
