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Documentation for CMol

Edit selection menu

The edit selection menu is the most powerful menu in the app. It allows you to make changes to the model in the display as specified by the options in the menu. Note that initially, everything is selected by default - if there is nothing selected under "filter by chain", for example, all chains are selected.

iPad menu

iPhone menu

1. Colour atoms: Tapping this leads to the Colour selection menu. Tapping a colour on this menu will allow you to recolour the selection to that colour without affecting the transparency.

2. Represent atoms: Tapping this leads to the Representation selection menu. Tapping one or more representations will allow you to change the representation of the selection. A few tips:

3. Transparency: tapping this reveals a transparency slider in a new menu. Moving this slider updates the transparency of your selection without affecting its root colour.

4. Filter by chain: all residues in a PDB file belong to a polypeptide or nucleic acid chain, and discrete polypeptide/nucleic acid chains have their own Ids. This menu lists the Ids and allows you to select one or more chains to filter by.

5. Filter by backbone: this menu will filter by either the main chain or side chain for both DNA and protein.

6. Filter by residue: this menu allows you to select individual residues to filter your selection by. A few tips:

7. Filter by secondary structure: this menu allows you to select by helices, sheets and loops.

8. Filter by element: this menu lists (only) the elements present in the PDB file and allows you to filter by the specified element.

9. Filter by atom types: "Standard atoms" refers to atoms contained within the polypeptide chains and nucleic acid chains. "Non-standard atoms" are those prefixed with "HETATM" in the PDB file, and include atoms of solvent molecules, ligands and prosthetic groups.

10. Change name: allows you to change the name of the selection.