The following steps are required to calculate the distance between a ligand and a particular amino acid in a protein.

Step 1: Open the PDB file in pymol 

Open PyMol and load the protein molecule which you have saved from the PDB. This is shown in figure 1. Go to simulator tab to find more about how to download and save the protein.

Figure 1: open PDB file in PyMol

Structure visualization in pymol

We can see two rows on the right side, labeled as ‘all’ and ‘2PTC’ where we can change individual appearance of a molecule as well as all molecules together. If there are multiple molecules, user can also select every molecule or object at same time.

User can also see A,S,H,L and C labels in the two rows as different columns, these alphabets implies, Action , Show , Hide , Label and Color respectively. We can use these GUI elements or the user can give commands to get performed actions which can be shown in Figure 2.

Figure 2: Structure visualization of pymol

 Viewing ligands through pymol

We can view the ligands which can present in a particular protein by ,Go to ‘A form ASHLC’ option in internal GUI, select ‘Present’ and ‘Ligands’ from that menu to view the Ligands present in protein.

 Figure 3 : Viewing Ligands through PyMol

The dotted line represents the ligand molecule.

Figure 4: Ligand representation 

Step 3: Calculate the distance between Ligand and an amino acid using pymol 

Go to wizard menu and select measurement. After that the user has to click on the atoms whose distance has to be measured. The distance will be displayed in yellow, with a yellow dotted line joined between the atoms. Here we are calculating the distance between the ligand and particular amino acid shown in figure .

Figure 5: Calculate the distance between Ligand and an amino acid. 

All the experiments done using:The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC.