Questions tagged [pymol]

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

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33 views

Pymol python script for selecting a residue's sidechain and calculating its center of mass

I trying to write a pythonic PyMol script that loads a PDB, cmd.iterates through the PDB and stores the residues (three letter code) into an array. I then want to loop through this array and ...
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1answer
31 views

How to show electrostatic interactions in Pymol on the wanted residue

I have the following Pymol visual, The green molecule is receptor and red/yellow is the ligand. In the ligand I highlighted Lysine (K) residue as yellow. What I want to do is to highlight and draw ...
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17 views

How do you search for new enzymes that are more stable for handling, immobilization?

Noob here. I get that I should deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, ...
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3answers
109 views

How to see effect of point mutation in PyMOL?

I am trying to model how a specific point mutation would affect the protein structure. So far, I've figured out how to create the point mutation in PyMOL using the mutagenesis wizard. I'm not sure ...
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1answer
140 views

PyMol: Output Polar Contacts Between Chains to Text File

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 determine polar contacts between chain A and all ...
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1answer
27 views

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
128 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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1answer
30 views

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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1answer
40 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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42 views

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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1answer
153 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
140 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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2answers
190 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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111 views

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
47 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
54 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
43 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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77 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
254 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
88 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
35 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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1answer
294 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
96 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
142 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
466 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
407 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
242 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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1answer
5k 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 ...