 Hi everyone. Welcome to basics and series. I'm your host Lokinder Kumar and today we're going to start the first video of our pie mold tutorial series that will focus on making publication quality figures using pie mold. As you already know that I have started this series to explain various settings that are available in pie mold, various tools that we can use to make nice protein structures and that we can use in our students reports, in the research articles and also in our projects. So right now what you're seeing on your computer screen is the interface of the pie mold software. So I'm going to show you that what are these different, different panels. For example in this particular window I can show you that on the top we have upper control panel. So this particular section is known as upper control panel. As you can see we have a lot of options that are available for us. For example we have file, edit, build, movie, display, setting and these all have various sub tabs that we can use to make the publication quality figures. On the right side what you're seeing is the object menu panel. In the object menu panel you can see A, S, H, L, C. Right now I don't have any protein structure here so I can't use that. So we're going to use those, those various different, different settings for object menu panel when we have the protein available in the display area. So and this is known as the display area. All right so if you are aware of this series I've already made one video how we can use protein data bank and what are the different features of protein data bank, what are the options available in the protein data bank, how we can download the files, structured files from protein data bank. So let's start by importing the structure using PyMol software. So one option was that you can download directly from PDB. Second option is you can use PyMol the control, upper control panel to download the structure file. So I'm going to use that particular option that is available in the PyMol software. So as you can see here this is the section where we can add commands. So if you are, if you are familiar with coding languages like Python or other languages you will find this particular section very, very convenient because using this particular section you can directly add commands and also you can write scripts and you can run your scripts on using that particular section. So we're going to start with the first command that I'm going to show you is fetch command. So write F-E-T-C-H fetch and it's going to grab the structure from PDB data bank directly and import that structure. So you need to provide the four letter code of the protein. In my case the four letter code is 2uv0. So it's a very simple command. Just write F-E-T-C-H and the four letter code and press enter. Now what you're seeing is the crystal structure, the three-dimensional structure of the protein of that particular four letter code. So this is very convenient that you can directly import the structure and you don't have to go and visit the website to download the structure. But if you do not know the code for that particular structure you need to visit the website for protein data bank and then download the structure from that particular website. Or you can note down the structure and use PyMole command line to import the structure. So first I want to move the protein and I'm going to see different parts of the protein. So how I can do that I need to press the left button on my mouse and then drag the protein in the direction I want to move. Right? So you can see I'm pressing the left click button on my mouse and I can move the protein in this direction as well as in the other direction. So this is how you can use the left click button on your mouse and then move the protein around. You can also use the same setting to move the protein in other directions. So this was the use of the left click button on your mouse. You can see I can move around the protein structure. It's really useful when you want to see different parts of the protein. Now what I can do with the right click button. So if I press the right click button and then move around try to drag what is going to happen it's going to zoom in and zoom out. So you can see I can go really close to the protein structure and see the various parts of the protein in either direction it's going to zoom in and zoom out. It's really useful when you're trying to see the ligands and trying to see the structures that are in the binding pockets of your protein. So this is very useful. Third important command is you can also use the scroll button in your mouse and then move the full protein and change its position on the display window. So if you press the scroll button and then drag your whole protein structure molecule will move. So I hope you understood that command that you can press the scroll the the central button present in between the left and right click button and then you can move the protein around. So it's very useful to combine all these mouse settings and then you know move around. So I can move around and if I want to change the position then I can I can zoom in and immediately I can zoom out and then also move the protein around. This was the first important thing that I want you to get used to while you are trying to make structures. Now let's go to the object menu panel which is present on the right side. Here what you're seeing is first is all and second is the 2uvo. So that is basically the structure of the protein that you imported. If I click on this one so right now I can't see the protein so it's turned off right. So now to see the protein structure I have to again click on this particular tab now the protein structure is visible. So I can see that now all my sub tabs A S H L C are active for this particular structure. What is A? A means action. When you click on this one you can see action is written and then you can perform various actions. One of the most used action is preset. In preset you have a lot of different options, sub options available and it will give you the settings for that particular option. For example if I want to use the preset for publication it will directly change my protein into a structure format that I can use for my publication. Now let's move on to the second tab which is S means show. In show tab what you have is you can see the structure of protein in various types of settings. For example you can see as a stick model, sphere model, ribbon model, cotton model. Let me show you one of the settings. For example I can show you the sphere model of the protein. Now what you're seeing here all the atoms that are shown here and they are the these spheres that are present in our protein structure. Now there are stick model of the protein. You can also see the stick model but you have to it is really important to know that you have to hide first. So there is another tab which is H means hide. So you can hide for example I can hide everything. So now I can't see the structure of protein then one by one I can show the first stick model then I will go back to the hide. I will hide everything then I will go back and then I will see the cotton model. Now you have color. So you can color the protein according to the the elements according to chains and right if you want to see different chains as a different color you can use this setting. So this is also pretty convenient to show different parts of the protein. Let me quickly show you some of the settings that I use for my protein structures. So first I will change the display. So I will go to display and I will change the background to you can change it to opaque. For now I will I will make it as a white background so so that it looks good on my document and then I will go to display I will change the quality. So I will do I will change it to maximum quality. So how I can save this image I can go to file and then export image as png. One option is that but if you are using a licensed version of pie mold you will have another option available right here which is draw ray session. If you click on this one and you can change the specifications of the image I will keep it like that and you can draw fast and you can raise slow if you raise slow your quality of the image will be high. So I'm going to press it and I'm gonna try to save a high quality image and now you can you can see that the background is no longer white and it's completely transparent and I can see some shadows. So this feature is only available when you have the licensed version of pie mold. So now the image has been saved in my document section I can copy that image from that and paste the image in my ppt file. So here is my ppt file let me zoom in and I will right click and paste the image. Now you can see the image clearly on the PowerPoint presentation and let me just crop the section the unwanted section of the image and let me zoom in and I'll show you the various features. So now you can see the structure of the protein and you can see your full domains you can see their ligands. So this is how you can make the final structure of the protein and you can save it as a png file and use in your presentations. In later videos I'm going to show you how to make different types of protein structure and how to show the ligand binding pockets how to show the labels for particular amino acids. So that and you can also change different different settings in that particular section. 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