[Jmol-users] no additional bonds

[Miguel H. <mt...@mt...>]

> how do I make sure no other bonds are added?
I sent out a memo on the auto-bonding behavior.

If you have bonding information in your file then no additional bonds will
be calculated.

The situation on .pdb files is somewhat complicated. Please read my Tech
Note and ask questions if it is not clear.

> And is this garuanteed not to change in the future?
Open source projects change. But as long as I am on the project I can
guarantee that we will not calculate additional bonds without explicit
requests from scripting commands.

> Can we introduce some
> sort of marker or command or whatever to establish a situation
> in which such a garuantee can be given? (That's what I liked
> about the "MathGraph" convention, it gave me that security.)

I can't imagine why a molecular visualization package would add additional
bonds that were not specified in the model file.

> And, more specifically, I need this certainty in a format that
> can also be loaded into Jmol with inline models.

From Jmol's perspective, there is no difference between an inline model (a
String), a file, or a URL. They all call *exactly* the same code.


Miguel