Questions tagged [pymol]
A python-based scripting language to visualise 3-D structures, especially of proteins.
38
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how to add a custom elements into PyMOL visualization?
I would like to add some 3D elements (balls and lines) to the PyMOL visualization to highlight some "holes" in the structure. Say I fetch 1tqn and I want ...
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Align two different structures with respect to their active sites or heme cofactor
I have two enzymes, with heme cofactors. but their overall structure is very different.
I use Pymol regularly to visualize protein pdb structures.
I want to align both structures, but the structures ...
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2
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1
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282
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calculate the backchain RMSD between two pdb files by pymol in Python
i have two protein pdb files and want to calculate the backchain RMSD between them. As far as I know the GUI of Pymol can use align to calculate the RMSD (but I don't know if it is the backchain RMSD)....
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Visualise multiple disappearing pdb files in Pymol
I have a sequence of pdb files which I want to load in pymol window so that it gives an impression of a video. I am using cmd.load function in a loop and deleting the loaded file in the next step. But ...
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2
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PyMol alignment script
Is there a way write a script in python to use "super" to align proteins from a 2D array? Each row of the array has 2 columns, and for each row, I want to "super" the two proteins (...
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How can I measure the distance between each pair of carbon alphas in overlayed protein structures?
I am trying to make a figure in which the protein structures are colored by the distance between the calphas in the overlayed structures.
I am comparing our cryoEM structure to that of a previous ...
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2
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665
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Pymol: select low confidence regions from AlphaFold pdb file
I have downloaded a predicted structure from AlphaFold as a pdb file (https://alphafold.com/entry/O75376) and loaded it into Pymol (2.3.0). There is quite a large portion of the structure that was ...
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Running into an error when loading Flexaid on PyMol 3.7
I have attached a screenshot from terminal, which is the result of me attempting to run Flexaid on my Mac.
I was wondering if anyone knows why this isn't running?
Thanks
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How can I list all amino acids in a protein using PyMOL?
What is the command in PyMOL for listing all the amino acids in a specific protein, say, 1a62.pdb?
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How do I build a glycosylated protein from PDB files manually?
I have a large protein PDB file (~3500 residues) and a couple of PDB files containing glycan structures I sourced from GLYCAM.
How can I attach the N and O-glycans onto each protein residue with ...
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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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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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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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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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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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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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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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179
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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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413
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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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2
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481
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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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696
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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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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 IDs that have to be extracted, and then run on dssp.
For the single chain extraction I tried several methods, such as:
...
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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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106
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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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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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387
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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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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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vote
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answer
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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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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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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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198
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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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411
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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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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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PDB file downloading: pymol automation vs. manual
I automated a PDB download using a Pymol script (below)
...
M__♦
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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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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 ...
user4378
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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 ...
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