Questions tagged [pymol]

A python-based scripting language to visualise 3-D structures, especially of proteins.

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How to show that one docking is better than another with Pymol visually

I have the following docking results: Dock_1 has better energy score than Dock_2. What I want to do is to show with Pymol that <...
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1answer
33 views

Programmatically adding hydrogen and remove water to multiple PDB files

I'm trying to dock a ligand to several hundred PDB files (receptors). I thus need to prepare the those PDB files like removing water and adding hydrogen. I can do that manually using Autodock or Pymol....
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Label and labelbox mismatched in Pymol after ray

I would like to ask how to overcome the problem of mismatched boxes and labels (pic). Is there an option focused on this? thanks Radim
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26 views

rmsd between re-docked complex and co-crystallized complex

I would like to calculate the rmsd between re-docked complex and co-crystallized complex for docking validation. How do I calculate the rmsd using Pymol? I tried the following command ...
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Ligplot: how to define path in Ubuntu

I installed Ligplot on Ubuntu and have a question. When I open a docking I get the error: Unable to create log file in temporary directory: C:/tmp . I already tried to change the path in several ways ...
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71 views

Loop Pymol command get_area

I want to select multiple residues from different PDB files loaded on the same pymol session. select resi LIG get_area sele How do I loop the above command to ...
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1answer
63 views

Assessing PyMol sequence alignment object

I use cealign in PyMol for structure alignment. Instead of visualization, I want to return the alignment object to my python script for further analysis. Is there a function to return the object ...
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1answer
83 views

Pymol: color spheres with different colors

Hello I am a Pymol user I want to color all alpha carbons (ca) and beta carbons (cb) from a certain ressidue in different color. How can I do this? I selected the spheres with: ...
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Using dssp after chain extraction

I have a list of PDB IDs with realtive chains that are to be extracted, and the run on dssp. For the single chain extraction I tried several methods, such as: ...
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1answer
39 views

Selecting part of an extracted ligand

I have the PDB 6LU7. I extracted the ligand using extract lig, org and then the protein using extract prot, poly. The ligand has three parts: 02J, PJE, and 010. I want to select the 02J and 010 ...
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1answer
47 views

Multiple input & output files?

I'm trying to print out the measured distances for each .pdbqt file, and then write a new output file for each .pdbqt, using the original name of the .pdbqt file as the new .txt file name. Below is ...
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1answer
42 views

Modify how a script prints the output?

I'm trying to print out all measured distances between a ligand and 2 residues (using PyMol), below is the script that I'm using. I only want to measure the distances between all the ligand's O & ...
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48 views

How do I color selective residues on the surface of a protein in pymol?

I am somewhat familiar with the pymol userface, but not very good with commands. I'm working with a pentameric subunit protein and I want to color specific residues on the surface of the protein, not ...
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1answer
128 views

Combine structures in the same session - PyMOL

I'm a student currently looking at antibody responses against a viral target protein of interest. I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody ...
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1answer
68 views

Outputting crunchable list of HBonds from Pymol

X-posted from the Main Stack Overflow because folks here are possibly more familiar with PyMol(?) I have been trying to assess the strength of an interface I want to mutate using Pymol. What I am ...
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1answer
29 views

What is PyMOLs search path for scripts?

I know I can run my PyMOL scripts if I specify a valid path from the current working directory and also using absolute paths, but can I have a central script repository, so I don't always need to ...
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175 views

Is there a way to save a full pdb file in PYMOL after uploading biological unit?

pdb code: 2obt The pdb file has a coordinates of a monomer. I have used following commands to generate an assembly, or in other words to upload one more ...
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1answer
75 views

Use a specific python.exe instance with PyMOL/Windows?

I want to use RDKit with a python script in PyMOL. RDKit requires a conda environment, so I think I need to be able to specify that the instance of python that I want to use would be in that ...
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1answer
93 views

pymol script to only select 5 chains within a distance from a reference and save the selection

I am generating 30 asymmetric units of a protein structure. Now, I want to select different combinations of 5 units which are 30 Angstroms away from the reference and save it as a different file. Here ...
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2answers
387 views

Putting labels of different sizes on one PyMOl Object

I'm new to PyMol (and StackExchange!) and working on my first project. I have the structure of a protein as an object, called PolyA-M, and the idea is that the residues of it are shown as spheres of ...
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2answers
311 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
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1answer
1k views

Get residue position from Pymol Selection

I can make a selection in Pymol using the resi parameter. Is there a way to get this resi data back out of a selection object? The only thing I found so far is how to get the position, as in the x/y/z ...
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1answer
196 views

Executing PyMOL from a Shell script

I'm trying to execute pymol from a shell script (and it is not working). I'm not executing the script on PyMOL but even if I do this, it doesn't work neither. However, if instead of a script the ...
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4k views

How to colour multiple residues in Pymol?

We can use color yellow, resi 3 color yellow, resi 3-8 to colour one residue or a range of residues. But what if I want to colour residue 3-8 and 10-20, how to ...