May 17 2013
To convert a chemical structure from 2D to 3D:
There are three ways in which to do this depending on whether you have a chemical in a chemical table or in the ICM workspace.
From the Chemistry/Convert/2D to 3D option menu option - convert a chemical in a chemical table.
If the compound is in the ICM Workspace:
If you have selected the compound as described above the "as_graph" option in the Object data entry box will suffice. You can decide whether you wish to keep the chemical geometry or optimize it in a force-field. Other options include whether you wish to add hydrogens and fix amide bonds.
From an ICM chemical table:
Once converted the compounds will be displayed in the 3D graphical display window and also in the ICM workspace.
Another way to convert all the ligands contained within a table (or a selection) into 3D coordinates :
To convert 3D representation in a molecular table back to 2D:
The protein data bank has not been storing any information about covalent bond types and formal charges of the chemical compounds interacting with proteins! This oversight makes it impossible to automatically convert those molecules to anything sensible and requires your manual interactive assignment of bond types and formal charges for each compound in a pdb-entry. Therefore, if you apply the convert command to a pdb-entry with ligands, the ligands will just become some crippled incomplete molecules that can not be further conformationally optimized.
Therefore, follow these steps to convert a chemical properly from a pdb form to a correct icm object. There are two ways to do this either via the ICM Workspace (recommended) or via the Graphical Display.
Change bond orders:
Change atom and charge:
Convert to 3D in MMFF force field:
To change the bond types in your ligand:
You can either select (see selection menu section)the atoms you wish to change graphically using the rectangular or lasoo selection button OR
You can select the By two atoms tabs and right click on the atoms you wish to change and then selecting the atom descriptor with the left mouse button as shown below.
To set the formal charge of a compound:
Click on MolMechanics/Edit Structure/Set Formal Charge and then select the appropriate charge.
The final step is to convert the compound into an ICM object:
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