[Jmol-users] failure to display partial bonds in JSmol

[Angel H. <ang...@ua...>]

Dear Bob, we found a very strange behaviour with JSmol (16.3.5, 16.3.19)

We have a web page, using WebGL modality (I don't expect that to be 
relevant, but...)

The conflicting file is SDF format, prepared with some other sofware by 
a colleague but saved to file using Jmol (Jmol-16.0429252053). It has 
two bonds with type 8 ("other" according to MOL documentation). Jmol 
application renders them as partial bonds (dashed); this is what we 
want. CORRECT

However, when loaded in JSmol using code in the page, the bonds display 
as solid single bonds. INCORRECT

When the file is dragged and dropped onto JSmol, they are displayed as 
dashed. CORRECT

We tried forcing the partial bonds using a script in line 3 of the file 
(either leaving bond type 8 or changing to 1).
jmolscript:connect (@4)(@5,@6) partial
The command works in Jmol but again fails in JSmol when the modified 
file is loaded via page code.

Magic: as soon as I open the console from the popup menu, the bonds are 
instantly displayed as dashed.

Any idea what is going on?

Attached prueba0.sdf is the original with bonds type 8, prueba1.sdf with 
bonds type 1 and script in 3rd line.

I can share the webpage privately if needed.

Thanks

·
  Dr. Angel Herráez
  Biochemistry and Molecular Biology,
  Dept. of Systems Biology, University of Alcalá
  E-28805 Alcalá de Henares  (Madrid), Spain
  https://biomodel.uah.es/