How to avoid bonds overlapped?

Hi,





I have a molecule from sd file and it is always displayed with a few overlapped bonds even when I have set the clean into optimized in 2D. If I mannually set in the applet on the html page to "optimized", it does relax the overlapped bonds. But it does not work when the option is preset in the javascript.





I have seen some informtion about avoid overlapping bonds in clean 2D extra options. But how to use it?





Appreciate.





Ben Li

The coordinates of your molecule may be wrong. Marvin does not generate new coordinates for the molecule if the structure already has got ones.


If you want to regenerate the coordinates durring the molecule loading, use the "importConv" paramater with the "c" option.


http://www.chemaxon.com/marvin/doc/dev/sketchman.html#parameters.importConv

Code:

msketch_begin("marvin",440,340); msketch_param("importConv","c"); msketch_param("mol","mymol.mol"); msketch_end();

Or you can regenerate coordinates in a molecule file with MolConverter.


MolConverter is part of both the Marvin Beans and the JChem packages.


Thus you can run it as a command line tool:

Code:

molconvert -2 sdf input.sdf > output.sdf

or access it from the API:


http://www.chemaxon.com/marvin/doc/api/chemaxon/formats/MolConverter.html