Atoms location in MravinSpace.

Dear all!

I'm trying to visualize  the structure of a polymer in MarvinSpace.

Firstly, I draw a structure in InstantJChem (see image 1 attached)

Then I copy it and paste to MarvinSpace. It draws some 3d structure (see image 2)

Is there any explanation on how MarvinSpace locates the atoms of this structure in the space? Does it take into consideration inter-atomic and inter-molecular relations in the chain, or it just "throws" it randomly? 

Regards,

Oleg Miloserdov.

Hi Oleg, 

the Generate3D module that performs the 3D coordinate generation is a force-field-based method, which takes inter molecular interactions in account. This method was developped to handle drug-size molecules. You can find a full documentation of the Generate3D (with explanation and examples) here:

https://docs.chemaxon.com/display/CALCPLUGS/Generate3D

If you have more questions, please feel free to ask us.

Daniel

Dear Daniel,

Thanks a lot for your help! 

 

Best regards,

Oleg Miloserdov.