3D templates and structures

User 870ab5b546

29-10-2014 17:24:31

I created an MRV file containing some 3D templates, which I've attached. I have a few problems with the implementation. First, see the screen shot; note that the templates are barely recognizable. Second, when I paste a structure into the drawing window, the ends of the bonds don't quite touch, making the structure a little harder to read. This is a general problem with the 3D structures, even when I generate them by 3D-cleaning a 2D structure. Third, notice that in the Newman projection, the bonds in the rear are visible; they are supposed to be made invisible (at least partly so) by the use of a blank alias for the C atom. Are not aliases implemented yet in M4JS?

ChemAxon f052bdfe3c

30-10-2014 20:42:07

"First, see the screen shot; note that the templates are barely recognizable."


You can add your own pictures (for example what you generated with Marvin beans) please see this example: https://marvinjs-demo.chemaxon.com/latest/examples/example-create-template.html here you cab add the URL of the picture into the icon field.


"Second, when I paste a structure into the drawing window, the ends of the bonds don't quite touch, making the structure a little harder to read."


The nice shadow on the bonds causes it, that we personally love, but it seems we should revise.


" Third, notice that in the Newman projection, the bonds in the rear are visible; they are supposed to be made invisible (at least partly so) by the use of a blank alias for the C atom."


We have implemented alias, but not for the blank case. Although, I think, you can  draw a structure in which the first carbon atom covers the one in the back. Can it work for you?


Best regards,


Efi


 



User 870ab5b546

30-10-2014 20:51:43










ehoffmann wrote:

We have implemented alias, but not for the blank case. Although, I think, you can  draw a structure in which the first carbon atom covers the one in the back. Can it work for you?





No, I need to hide the portion of the C(back)-H bonds that are inside the circle. See the picture. If you can make the circle hide the bonds and atoms behind it without hiding the atoms and bonds in front of it, that would work, too.

ChemAxon 996dedebe0

10-11-2014 07:03:19

Dear bob,


The ellipses can have a background property. Unfortunately Marvin Desktop does not order them by Z coordinates, but Marvin JS does! So you can use this feature to achieve your goal. See the file attached.

User 870ab5b546

10-11-2014 13:53:33

Perfect! And that means I no longer need to worry about having a space character as an alias of for the C atom in the back!