How to convert structure smiles into structure coordinates

How to convert structure smiles into structure coordinates

When you open a .smi file which contains SMILES structures through
File > Open, Marvin automatically loads it and assigns 2D coordinates to
the structure. You can extract these 2D coordinates through Edit > Source
panel, choosing e.g. MDL file format with Edit > Source > View > MDL.
You can refine these coordinates with Structure > Clean2D. If you want 3D coordinates, you can use Clean3D in Marvin.

Best Regards,

Efi

May I add some 3D hints more:

Before using "Structure - Clean 3D - Clean in 3D" it's good to define in this menu the "Cleaning Method". In most cases the best option is "Fine with Hydrogenize". The option is stored and used once more after opening MarvinSketch the next time.

Marvin is using an optimized Dreiding force field method.

If you want to have a structure without hydrogens, simply use "Structure - Remove - Remove Explicit Hydrogens", but do it after optimizing.

Then you can save the structure as "MDL mol file". Nearly all programs are able to read this, especially Jmol

Best regards, Hans-Ulrich