From: Michael T Howard <mth@mt...> - 2004-01-21 20:52:02
> I just downloaded Jmol 10 pre 5 and am using the applet on my
> webpage. The graphics are beautiful!! I especially like the atom
> There is, tho, one feature I don't understand - some of the
> bonds are drawn as "dashed" bonds. Is this intentional, perhaps having
> to do with the bond length?
Damn. I made an 'enhancement' and I fear it is coming back to bite me.
Nick Greeves had the same problem with the 'dotted bonds'.
The problem is that your .pdb files are not following the PDB spec. Those
'dashed bonds' are hydrogen bonds.
The PDB specification clearly states that there can only be 4 covalent
bonds per CONECT record. The following fields are for hydrogen bonds. If
an atom has more than 4 covalent bonds then you have to have an additional
> And you can't change the width of the dashed bonds.
Actually, you can:
Patrick, do you know which program exported the files that you are looking
at? Can you send me an example?