MOptima
Chapter 05

Importing and Building Molecules

Main entry points

MOptima supports three practical starting routes:

  1. Draw a molecule.
  2. Input a SMILES string.
  3. Open an existing structure file.
You can begin from a drawn structure, a SMILES string, or an imported file, depending on what information you already have.

Draw a molecule

Use the drawing workflow when you want to sketch a new structure manually. This route is useful for quick ideation, small organic systems, and structures that are easier to define graphically than by file import.

Input SMILES

Use the SMILES dialog when you already know the connectivity in text form. This is often the fastest route from a literature structure or notebook idea into a 3D-editable model.

Open a file

Use file import when the geometry already exists and you want to continue editing or calculation from that structure.

Multiple molecules

When an import contains multiple SDF records or disconnected fragments, MOptima asks whether to open Batch Mode.

  • Choose Yes (Batch Mode) to keep separate structure cards and work through them one by one.
  • Choose No (Keep as one) to show every molecule together in the normal Editor. Overlapping fragments are translated rigidly so the initial distance between molecules is at least 3 Å.

Use Import -> Add to Current Editor to add a drawn molecule, SMILES input, or SDF to the current non-batch structure. Existing atoms stay fixed and only overlapping additions are repositioned. This submenu is unavailable in Batch Mode.

After import

After any import route, do the same short validation pass:

  1. Inspect the 3D structure.
  2. Use the Edit panel if the geometry needs correction.
  3. Confirm atom picking works as expected.
  4. Save the project before large calculations.
After import, inspect the loaded geometry in the viewer before moving to editing or calculations.