ANY bonds in Marvin

I have this source:

Code:

<?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2"           elementType="Br O"           formalCharge="1 -1"           radical="monovalent 0"           x2="-11.841666221618652 -8.434999427795411"           y2="1.2833333015441895 1.225000023841858"           />       <bondArray>         <bond atomRefs2="a1 a2" order="1" queryType="Any" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

When I make a JPEG out of it, it shows the "any" bond as a dashed line; but when I display it in Marvin, there is no bond visible at all between Br and O. Is there a MarvinSketch parameter that will make the "any" bonds appear as a dashed line?

There are 3 options at any bonds drawing: Auto, Dashed line and Solid line.


You can set it from the Preferences menu (Edit/Preferences/Bonds).


You can also control it programatically: give the sketchAnyBond (applet) parameter or use the UserSettings.setSketchAnyBond(String) method.


By the way, at some kind of scaling factor, the any bonds may be unvisible under OS X. It is an OS X specific bug. We will solve it as soon as possible.

Tamas wrote:

There are 3 options at any bonds drawing: Auto, Dashed line and Solid line. You can set it from the Preferences menu (Edit/Preferences/Bonds).

I tried this method. When I set the ANY bond to solid, the bond becomes solid, but when I set it to Dashed, it remains invisible. Perhaps this is the OS X bug you mentioned. The scale is 32.





The sketchAnyBond applet parameter is not documented at http://www.chemaxon.com/marvin/doc/dev/sketchman.html. That's why I didn't know about it. I assume the string may be "automatic", "dashed" or "solid"?

Quote:

The sketchAnyBond applet parameter is not documented at http://www.chemaxon.com/marvin/doc/dev/sketchman.html. That's why I didn't know about it. I assume the string may be "automatic", "dashed" or "solid"?

I have completed the documentation: http://www.chemaxon.com/marvin/doc/dev/sketchman.html#parameters.sketchAnyBond