Are you struggling with adjusting the viewing perspective of your protein structure in PyMOL? In this tutorial, we'll show you how to make a 3D view linear in PyMOL to create a clear and accurate representation of your molecular models.

Step 1: Open your protein structure

First, open your protein structure in PyMOL by loading the PDB file or using the fetch command to retrieve a specific protein structure from the Protein Data Bank.

Step 2: Adjust the display settings

Once your protein structure is loaded, navigate to the Display menu and select the Graphics item. In the Graphics window, locate the 'Field of view' parameter and set it to a low value (e.g., 10) to create a more linear perspective.

Step 3: Set the camera angle

Next, navigate to the Display menu and select the 'Settings' item. In the Settings window, go to the 'Viewing' section and adjust the 'Camera angle' parameter to a low value (e.g., 10) to minimize perspective distortion and create a linear 3D view.

Step 4: Fine-tune the view

You can further fine-tune the 3D view by adjusting the rotation and translation of the protein structure. Use the mouse or the command line to rotate and translate the view to achieve the desired linear perspective.

Step 5: Save the view

Once you have adjusted the viewing settings to create a linear 3D view, you can save the view by going to the Display menu and selecting the 'Save orientation' option. This allows you to easily return to the linear perspective view in future sessions.

By following these simple steps, you can make a 3D view linear in PyMOL to ensure accurate and visually appealing molecular visualization of your protein structures. Whether you are a beginner or an experienced user, mastering the art of adjusting the viewing perspective will enhance the quality of your molecular models and facilitate insightful analysis.

So, next time you're working with protein structures in PyMOL, remember these tips to achieve a clear and linear 3D view. Happy modeling!