molconvert adding hydrogens

molconvert seems to add Hydrogens when I creat a Jpeg or a name is there any way to stop this ?





Ie if I'm using radical species

Could you please try the H_off option like:

Code:

echo "[CH2]CCC" | molconvert "jpeg:H_off" - -o radical.jpg

You can read more about image export options at:


http://chemaxon.com/marvin/doc/user/images-doc.html


http://chemaxon.com/marvin/doc/dev/formats.html

Hi Thanks,





Thats almost what I want.





There really needs to be an option to show the hydrogens explicitly detailed in the molecule file. So that radicals can be dealt with. Also the software currently assumes alot of the molecules are cation/anions. You should be able to tell the software they are radicals and it should put put a C(dot) rather than C+ C-.





But still a very very useful tool. keep up the good work





thanks roger

Hello, you can add a dot, if you select an atom, right-click on it, and select the "Radical" menu. You can select monovalent/divalent etc types of radicals. You can also control the explicit/implicit hydrogens (or more precisely their visualisation) in the View/Hydrogens menu.





If you are converting molecules from other sources (i.e. from third party SDF files) you can use Standardizer to set up transformations and convert existing structures to a common form (like converting charged carbons to radicals), see: http://www.chemaxon.com/product/standardizer.html