3D editing of molecules

Hi,


I know there are other programs to edit molecules in 3D but it would be a nice feature to have the possibilty to change bond lengths, bond angles and dihedral angles in a molecule. Using "Clean 3D" does not always give the conformation you want to have.


I got this desire evaluating the topic "Conformers and energies...", see http://www.chemaxon.com/forum/viewpost16238.html#16238





Regards, Hans-Ulrich

See this post.

Hi, and how to integrate this plugin in the editor without using the applet ?


I would like to have it in a MarvinBeans 3D editor.





Regards, Hans-Ulrich

It's not a plugin, it's a Java program.





The only way to get it integrated into a MarvinBeans editor is to beg ChemAxon to incorporate it.





Meanwhile, the program works.

Hi bobgr, yes it works fine.

Quote:

The only way to get it integrated into a MarvinBeans editor is to beg ChemAxon to incorporate it.

Yes, so I will beg ChemAxon to incorporate it.





Regards, Hans-Ulrich

Hi Hans-Ulrich,





MarvinSpace can change the torsion angles using the dihedral angle monitors. The feature is not well-documented, so I try to briefly summarise it here:





1. add a dihedral monitor to the scene: press the torsion angle measurement button in the toolbar (3rd icon), then click 4 atoms => the dihedral monitor is displayed





2. click the semi-circle around the torsion => it's colour changes from green to yellowish and it's displayed a bit shifted (if the dihedral angle label obscures the semi-circle, then the label can be dragged away by the mouse)





3. now press and hold shift+control and use mouse dragging to rotate one side of the molecule around the rotatable bond (if you click the torsion monitor twice, then the yellow circle is shifted to the right and the other side of the structure is rotated).





Please note, that the torsion monitor is updated on-the-fly (that's why it's called a monitor and not a simple label), and similarly, if you add other monitors (distance, angle) to your molecule, than those are also updated instantly.


Unfortunately, bond lengths and bond angles cannot be changed in mspace.





Another nice feature: if a surface is also displayed and some properties like electrostatic potential is mapped onto the surface, then the surface and the mapping is also updated on the fly as the molecule is rotated about the rotatable bond.





Hope it helps and you like it.





Kind regards,





Miklos

Hi Miklos,





thank you for your tip. I used this procedure immediately to produce the glycerol conformer discussed in the other topic on calculating geometries: ( http://www.chemaxon.com/forum/viewpost16277.html#16277 ).





This fine feature should be available in MarvinSketch also. I like it.





Best regards, Hans-Ulrich

I would also very much like to see this feature in MarvinSketch.

Actually, we have plans to do the opposite: develop MarvinSpace further to turn it to a 3D structure builder. Wouldn't that be useful and attractive in your application?





Miklos

I would rather not have to teach the students to use a new applet. Besides, one feature that makes Marvin so powerful is the ability to switch back and forth between 2D and 3D capabilities. I have no objection to expanding the abilities of MarvinSpace, but I would very much like to see you extend Marvin's 3D capabilities.

Hi,


I also would like to have the 3D editing feature in MarvinSketch. To teach different molecule editors is impractical.





There are in MarvinSketch the possibilities to activate 2 atoms for a bond, 3 atoms for an angle and 4 atoms for a dihedral angle, see screenshot, so it should be easy to incorporate "handles" for this coordinate parameters.





And one argument more: Handling molecules in MarvinSketch is more convenient than in MarvinSpace.





Regards, Hans-Ulrich

Hi Hans-Ulrich and Bob,





We decided to implement 3D editing features into MarvinSketch for bond lengths, bond angles and dihedral angles. Depending on our capacity, these features will be available in Marvin 5.2 or 5.3.





If you don't mind, we will contact you for collecting use cases when we start the development.





Best regards,





Akos