When I try to install pymol using conda install -c schrodinger pymol-bundle as the documentation instructs (https://pymol.org/2/), an error occurs, an ...

I have a PDB structure that I'm analyzing which has a putative binding pocket in it for some endogenous ligand. I'd like to to determine for the rele ...

I am using PyMol and as of now I have to write a long command to delete useless files after splitting states: I want to avoid deleting posesD01_000 ...

I would like to know if there is any way to click or any command that I can use to find a particular amino acid sequence in PyMol. Now it is quite tim ...

Specifically, when runnning fetch 2mi1 3zkt cealign 2mi1, 3zkt I get the following error: CEalign-Error: Your target selection is too short. If ...

I am new to PyMOL but have a very specific task that I need to do. I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to d ...

I currently have a protein which is the focus of my study (.pse file) and several ligands (.pdb files) that I wish to bind to this protein to view whe ...

I am doing some tutorial on protein modeling by using multiple templates to model the same protein. I am currently trying to run the align_all.py howe ...

I am trying to load an mrc file, generate the map of it and then save the image, the problem is that it only saves a blank image, the code I run is th ...

I am a beginner to PyMOL and I am using it for my docking project. I have encountered errors using the Autodock/Vina plugin in PyMOL. I was trying to ...

I just tried to create a small Python script that first installs a certain package (PyMOL), based on the Python version installed on the system and th ...

A few days ago I had some issues with one program (adt from MGLTools) I was using without any problems for the last couple of months. I wanted to rein ...

I am trying to install the open-source version of PyMOL on a mac through the Homebrew package manager as recommended on the official website: https:// ...

I'm new to PyMOL, and I'm trying to write a python script that will generate a .txt file and save a PyMOL command output to it. Let's say it has an ar ...

I work on lipid and water structure. I have to select every water (group 1) that is below 4A from the lipid (group 2). I used this command: Unfortu ...

I am following this step to print the residues that I selected in pymol, and I found that some of the residues got iterated more than 1 time. Does any ...

I have maybe more technical question than code-related. I try to perform PCA (with MDAnalysis package) with only PDB file - this pdb file contain 100 ...

I am using Biopython to perform various operations on a pdb file. Subsequently I would like to add some new atoms to the Biopython structure object ge ...

I am writing parser to parse PyMOL files (language for bioinformatics). I know that double-quote char makes a string like "text". But single-quote cha ...

I have been unable to only color the residue of a specific chain in Pymol. Sorry, this seems to be a clear Beginner's question. So far, I am only abl ...