Here we are calculating the distance between the ligand and particular amino acid shown in figure. The distance will be displayed in yellow, with a yellow dotted line joined between the atoms. After that the user has to click on the atoms whose distance has to be measured. Go to wizard menu and select measurement. Step 3: Calculate the distance between Ligand and an amino acid using pymol The dotted line represents the ligand molecule. 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. We can use these GUI elements or the user can give commands to get performed actions which can be shown in Figure 2.įigure 2: Structure visualization of pymol 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. If there are multiple molecules, user can also select every molecule or object at same time.
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.
PYMOL TUTORIAL MEASURE BOND DISTANCE HOW TO
Go to simulator tab to find more about how to download and save the protein. Open PyMol and load the protein molecule which you have saved from the PDB. The following steps are required to calculate the distance between a ligand and a particular amino acid in a protein.
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