 Hi everyone, welcome to basics and series. I'm your host, Lokendra Kumar and today I'm going to show you how to export ligand molecules from a protein structure. If you're aware of this series, I have already made a introductory video on PyMol where I have shown how to use basic settings in PyMol, what is upper control panel, what is object menu panel and what are different different mouse settings that are going to help you while you are analyzing your protein structure. So if you're new to the channel, please subscribe to the channel, and if you like the video, please press the like button. All right, so without delay, let's start exporting the ligand molecule from a protein structure. To export a ligand molecule from a protein structure, we need a protein structure and for that, we need to use a command called fetch command. So we are going to go to the command line and we're going to type FETCH space. Now, you need to type the four letter code of your protein. In our case, it is 2UV0. So I'm going to type FETCH space 2UV0. I'm going to press ENTER. Now you can see the protein structure is visible in the PyMol display window and this is a protein called LASR. This is a protein of pseudomonas eruginosa quorum sensing system and plays a very important role in bifilm formation. So next step to export the ligands, we need to see where the ligands are. So first, I would like you to understand the structure of protein. It is helpful to export the ligand if you know what is the structural features of your protein. In my case, it's a tetrameric protein and I know that all four domains, they are similar and they all contain one ligand molecule. So what I'm going to do is first I'm going to remove these red dots. These red dots are the water molecules. For that, what I'm going to do is I'm going to go to the object menu panel, which is present on the right side. I'm going to go to the A action command and then remove water. So immediately you'll see that those red dots, they are no longer available. Now the next step is I'm going to select the chains. For that, I'm going to go to the mouse mode here and you can see there is a tab called selecting. I'm going to click on that one and you can see now there is a change in this particular tab. Now I can see chain. If you can keep pressing this particular option, you will see objects, you will see molecules, you will see C alpha, you will see atoms, you will see residues. So I need chains because I want to select specific chains in this case. So I will make sure that it is showing me the option of chains. Then I'm going to select three chains because I know that these four chains are identical and then I'm going to go again to my selection tab and press on A and remove atoms. Now, I have only removed the chains. So the ligand is still there. So I also need to remove these extra ligands for that. I'm going to go again to the mouse control panel and I'm going to select residues because now I'm selecting ligands. So I need to change it to residues. After that, I'm going to click on these ligand molecules and again I'm going to go to the selection SELE to the action panel and I'm going to remove the atoms. So now you can see I have removed three ligand molecules as well as three protein molecules. So that it appears on the center of your display window, you can right-click and you can see various commands. They will pop up and I will use zoom with command that will immediately brings the protein molecule to the center of the display window. All right. So the next step, what I'm going to do is again, I'm going to select the chain and remove the chain because as I have mentioned that the objective is to save the one ligand molecule in this case. So after selecting the chain, I'm again going to go to the object menu panel to the selection tab and again to the action and then remove atom. Now you can see only the ligand molecule is visible. So everything is deleted. You can also again zoom with and see the ligand molecule closely and the next step is to save this particular molecule. So what I'm going to do is I'm going to go to file, then I'm going to go to export molecule. This particular option will give me a pop-up window which is save molecule window and I'm going to go to save directly. After pressing this, this is going to give me a particular folder where I'm going to save it in this particular folder which is documents in my case. You need to change the file type. So select the second option which is PDB and it's not a PDB CIF. Just select the PDB one and then name the ligand molecule. In this case, I'm going to name this molecule as ligand and then press enter. Now your molecule has been saved. How you can access that molecule, you can go to the particular the same folder that where you have saved the molecule. In my case, this is documents. So I can see I have a ligand PDB file. If I double click on that one, a new window, pie mold window will appear and I can see ligand molecule. So now you have a PDB file of the ligand molecule and this file you can use for various different things. You can use this for molecular docking. You can use this for structural analysis and which is pretty convenient if you don't have the PDB structure of the ligand. So this was the shortcut way you can export ligand molecules from a pie mold or a PDB protein structure. So I hope you liked the video and it was helpful for you to export here ligand molecule and if you liked the video, please press the like button and if you're new to the channel, please do subscribe to the channel. Thank you and take care.