Emilie Meyer
PyMOL is a powerful program with a complex interface that can be daunting for new users. It is a program meant to be explored and played with, and it is used to display 3D models that can be manipulated by the user. The program has two windows: the External GUI, which contains the menu bar, shortcut buttons, and the command line; and the PyMOL Viewer, where the 3D models are displayed and interacted with. Users can rotate, translate, and manipulate the models, as well as adjust viewing modes, colours, labels, and more. While PyMOL has default settings, users can also input commands to customise their experience. This includes using the mouse buttons to handle rotations and translations, and using the command line to input Python expressions.
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What You'll Learn
Navigating the interface
PyMOL has a powerful and flexible interface, but it is complex and can be daunting for new users. When you open PyMOL, two windows will appear. The first, smaller window is the "External GUI", which contains the menu bar, shortcut buttons for common commands, and the command line. The second window is the PyMOL Viewer, where 3D models are displayed and where you can interact with and manipulate the model.
The PyMOL Viewer is where you can rotate and move the model. You can also change the view by clicking and dragging the protein. The left mouse button handles rotations, the middle mouse handles XY translations, and the right mouse handles Z translations. The model's x and y axes are horizontal and vertical, respectively, and the z-axis is perpendicular to the screen.
Above the mouse control panel is a list of current objects and buttons for actions, show, hide, labels, and colours. These buttons are shortcuts for most of the simple command syntax. The buttons include Reset (reset view), Zoom (reset zoom), Draw, Ray (ray-traces the current view), and Rock, which waggles the structure slowly back and forth about the vertical axis.
The text window at the top right shows the output of the PyMOL/Python interpreter as it responds to commands that you have typed. You can type these commands in the graphics window or in the PyMOL> text box below the text panel. PyMOL will try to read and interpret any command you type almost anywhere.
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Selecting and manipulating objects
PyMOL is a cross-platform molecular graphics system that provides an interactive, visual environment for exploring and analysing 3D structures of proteins, nucleic acids, and small molecules. It allows users to select and manipulate specific atoms or groups of atoms within these molecules.
There are two main approaches to selecting regions in PyMOL: using the graphical user interface (GUI) or the select command. The former involves physically clicking on the regions of interest in the viewer window, while the latter is prompted at the command line. Once a region is selected, it is highlighted with pink boxes, and a new object (sele) appears in the object menu panel. From here, you can grow or reduce your selection by clicking on additional residues or clicking a second time on a selected residue, respectively.
To save a selection, select 'rename' from the A menu and type the name. You can then modify the properties of the atoms within the group using the available pop-up menus. For example, to change the representation of a selection to sticks, you would use S -> as -> sticks.
PyMOL also allows you to perform actions on specific groups of atoms. For instance, you can select active-site residues in a protein to highlight them in another colour. Additionally, you can use the alter command to make changes to assignments made by dss, followed by 'rebuild'.
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Changing views and perspectives
PyMOL is a complex program with a powerful and flexible interface that can be daunting to new users. It is designed to visualise 3D models of molecules and their atoms, which are loaded from detailed coordinate files.
The PyMOL Viewer is where users interact with the 3D models, rotating and manipulating them. The program is designed to run on older computers, so the maximum quality is not enabled by default. To change this, users can select Display, Quality, Maximum Quality, which results in rounder shapes, smoother curves, and better colour shading.
The program also offers an Object Control Panel, which allows users to adjust viewing modes, colours, labels, and hiding options. The Object Control Panel also allows users to select parts of the model by clicking or dragging, and these selections can be saved and renamed.
To change the view in PyMOL, the program moves a "camera" to change the view of all objects simultaneously, rather than moving the objects relative to one another. This means that the model's axes may no longer correspond to the directions of the screen. Users can also rotate, translate, and transform selections using commands or the mouse in editing mode.
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Modifying colours and labels
PyMOL offers a variety of options for modifying colours and labels. Labels can be modified per object or per selection, and the colour of the label text can be changed. For example, to set the label colour of an object to green, you would use the following command:
> set label_color, green, object_name
You can also set the colour of a specific atom within an object:
> set label_color, yellow, /protein/A/A/23/CA
The font size of labels can be adjusted using positive or negative numbers, with the default size being 14 points. For example, to set the label size to 2 angstroms, the command would be:
> set label_size, -2
In addition to modifying label colours and sizes, PyMOL allows users to customise the font, outline colour, position, and shadow of labels. The position of labels can be controlled using the label_position setting, which adjusts the placement in camera X, Y, and Z coordinates. The label_outline_color setting improves contrast and readability by drawing an outline around each character.
PyMOL also enables users to modify the colours of objects or atom selections. Colours can be set to predefined named colours, RGB hex colours, or colour ramps. For example, to set the colour of an object to a predefined colour:
> set color, red, object_name
Alternatively, to set the colour of an atom selection to an RGB hex colour:
> set color, #FFFFFF, selection
These are just a few examples of the colour and label modification capabilities available in PyMOL.
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Saving views and images
PyMOL is a powerful and versatile tool for creating high-quality images of molecular structures. It is widely used in publications and presentations. The process of saving views and images in PyMOL is quite straightforward and offers a lot of flexibility in terms of quality and resolution.
To save a view in PyMOL, you can use the "view" command followed by a key and an action. The action can be either "store" or "recall", with "recall" being the default option. Here is an example of the command: "view 0, store". This command will save the current camera view. You can also use the function keys F1 through F12 to save and restore views.
Now, to save high-resolution images in PyMOL, you can use the command line or the graphical user interface (GUI). First, open PyMOL by typing "PyMOL" in a terminal or by double-clicking the shortcut. Then, go to "File --> Open --> Select an input PDB file". Here, you can set parameters such as background colour, view, etc. If you want to set a background colour, you can do so through the GUI by going to "Display --> Background --> White" or by using the "bg_color" command in the command line.
To generate a high-resolution image, you can use the "ray" command in the command line. This command will initiate the ray-tracing process, which generates an image of the current scene. You can also specify the dimensions and resolution of the image using the "ray" command. For example, "ray 2400,2400" will create an 8-inch square photo at 300 DPI. Alternatively, you can use the "PNG" command with the dpi setting to achieve similar results.
Additionally, you can adjust the view of the molecule or protein structure before saving the image. You can use your mouse to get the desired view or use the command line for more precision. The "orient" and "center" commands in PyMOL can help you properly orient and centre your system in the interface. You can also use the "set ray_trace_mode" command to choose from four different ray trace modalities.
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Frequently asked questions
PyMOL offers a complex interface that can be daunting to new users. The left mouse button handles rotations, the middle mouse button handles XY translations, and the right mouse button handles Z translations.
To change the view, PyMOL moves the "camera" to view all objects simultaneously. The model's x and y axes are horizontal and vertical, and the z-axis is perpendicular to the screen. The camera can be moved using the commands rotate, translate, and transform_selection, or with the mouse in editing mode.
Once you have found the appropriate view, you can save an image by selecting File, Save Image. The image will be saved in PNG format.
