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PyMOL is a powerful molecular visualization software that also allows users to edit molecular structures. Here are some ways to edit structures with PyMOL: If you are new to Pymol, I would recommend practicing  here . I can also recommend you slightly expert-level tutorial  here . 1. Add Atoms and Residues: To add atoms or residues to a structure, use the "Builder" function. First, select the residue or atom you want to add to. Then, go to "Wizard" > "Builder" and choose the atom or residue to add. 2. Delete Atoms and Residues: To delete atoms or residues from a structure, use the "Delete" function. First, select the atoms or residues you want to delete. Then, go to "Actions" > "Delete" and confirm the deletion. 3. Mutate Residues: To mutate a residue to another amino acid, use the "Mutagenesis" function. First, select the residue you want to mutate. Then, go to "Wizard" > "Mutagenesis...

Pymol is a powerful and versatile molecular visualization software that allows users to create high-quality 3D representations of molecular structures. Here are some specialized tricky and magical codes of Pymol. If you are new to Pymol, it is highly advised to practice  Basic Pymol Tutorial . In case you are looking to learn structure editing in Pymol, please follow  here . 1. Tricks Displaying secondary structure The following code displays the secondary structure of a protein using a color code where alpha helices are red and beta sheets are yellow. show cartoon set cartoon_ring_mode, 3 set cartoon_ladder_mode, 1 set cartoon_fancy_helices, 1 color red, ss h color yellow, ss s 2. Aligning structures The following code aligns two structures based on their alpha carbons and displays the aligned structures in different colors. align 1abc and chain A, 2xyz and chain B color blue, 1abc color green, 2xyz 3. Creating a surface representation The following code creates a surface rep...

PyMol is an important package for analyzing and generating publication-quality or high-quality images. After reading this tutorial, you will be able to generate simple ribbon diagrams with labels if required. Generating specific surface representation to your system and the last section is all about how to generate high-quality figures of protein and ligands. The current document is a basic tutorial and those who are already familiar with Pymol are advised to follow  here.   Before going to the following sections, you are required to load your PDB file, and change your display color to the one intended. Display --- Background How to read the below part, if you are new? A sentence that starts with "#" is just an explanation of the code present in the very next line. Pymol offers you two parts in the GUI interface, and you can use the below codes in any interface. 1. Tutorial on generating a ribbon diagram and adding labels: # Load a protein structure load protein_name.pdb # Sh...