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4 votes

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

So on the GUI form of PyMOL on the right hand side you have a list of what is ambiguously called objects in PyMOL (models elsewhere), which can be enabled or ...
Matteo Ferla's user avatar
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4 votes
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PDB file downloading: pymol automation vs. manual

To expand on the comment by marcin: fetch downloads files in mmCIF format by default (https://pymolwiki.org/index.php/Fetch). Not all PDB entries have PDB format ...
jgreener's user avatar
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4 votes

How to show electrostatic interactions in Pymol on the wanted residue

Depends whether you work with named selections which is preferable and helpful if you want to use this Pymol session for future images. In this case, use the distance command for your two selections, ...
bunher's user avatar
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3 votes
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How to colour multiple residues in Pymol?

Note: as I don't have any working version of pymol at the moment, I am not able to test the solution properly. However, an easy way is to first create a selection, and then to color it: ...
Mitra's user avatar
  • 504
3 votes

How to see effect of point mutation in PyMOL?

A common metric used to assess if a mutation destabilises the structure is the difference in Gibbs free energy. PyMOL does not give a ∆∆G (difference in Gibbs free energy, kcal/mol), but a very crude ...
Matteo Ferla's user avatar
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3 votes

Loop Pymol command get_area

from https://www.blopig.com/blog/2019/08/how-to-iterate-in-pymol/ Example 1: Print the names of all the selected objects You’ve selected several objects in PyMOL, and you want to see their names. By ...
pippo1980's user avatar
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2 votes
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Get residue position from Pymol Selection

Ok, after some more searching I found the answer. You have to use the cmd.iterate function to iterate over the default selection ("sele", first parameter). With the second parameter you can push the ...
C. Zeil's user avatar
  • 121
2 votes

Putting labels of different sizes on one PyMOl Object

'label_size' is a object-state-level setting, which means that you will have to rely on the 'create' command to create a new object for every different label size. It can certainly be automated, and ...
bunher's user avatar
  • 71
2 votes

Programmatically adding hydrogen and remove water to multiple PDB files

I believe PDB2PQR CLI will do the work wonderfully. Don't let the name trick you: PQR files are organized like PDB ones. Under the hood it runs propka, which is state-of-the-art for predicting a ...
O.Laprevote's user avatar
2 votes

PyMol: Output Polar Contacts Between Chains to Text File

So you can install PyMOL as a standalone, but you can also install it as a bona fide Python 3 module via conda: ...
Matteo Ferla's user avatar
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2 votes

How do I build a glycosylated protein from PDB files manually?

You can use ChimeraX. Open your glycans and your protein pdb files as different models, then move the models of your glycans until they are near the residues you want (in the Toolbar: Right Mouse -&...
O.Laprevote's user avatar
2 votes

How can I list all amino acids in a protein using PyMOL?

At the command, change the current directory to your target directory: cd my-directory-path-containing-my-files Load the file: ...
Supertech's user avatar
  • 596
2 votes
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Pymol: select low confidence regions from AlphaFold pdb file

Answer from @matteo-ferla, converted from comment: They are stored as b-factors. This is well described in the PyMol wiki. [please edit to improve this answer, if possible]
2 votes

calculate the backchain RMSD between two pdb files by pymol in Python

The backbone can be specified using a selector for the names of these, which are N, CA (Cα) and ...
Matteo Ferla's user avatar
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2 votes
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how to add a custom elements into PyMOL visualization?

my attempt : ...
pippo1980's user avatar
  • 1,043
1 vote
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Pymol python script for selecting a residue's sidechain and calculating its center of mass

I am guessing you used the command pymol.cmd.centerofmass? If so the selector is the ticket to doing it by selecting everything of the residue bar the backbone ...
Matteo Ferla's user avatar
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1 vote

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

From your title, you are after better immobilisation, i.e. your enzyme behaves poorly when bound. Poor thermostability: Engineering enzymes for better thermostability, involves predicting mutations ...
Matteo Ferla's user avatar
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1 vote

How to see effect of point mutation in PyMOL?

You could give SAAPpred a try. This tool uses machine learning (in the form of random forest) to predict the local effects of a single point mutation on the protein ...
fra's user avatar
  • 567
1 vote

How to see effect of point mutation in PyMOL?

You could run a molecular dynamics simulation for example with Gromacs or Charm. The problem with pymol is that the structure is static and you don't know how much tension that point mutation creates. ...
Soerendip's user avatar
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1 vote

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

maybe you can use the "per-residue interaction scores" (wich is available via Schrödinger). On the other hand,to show if a Docking Pose is really "better" you could show specific ...
Lucas's user avatar
  • 136
1 vote

Label and labelbox mismatched in Pymol after ray

It is a glitch in PyMOL. Caveat. I would say that, whereas cmd.label is great for adding labels en-mass for internal figures, it is not great for figures for ...
Matteo Ferla's user avatar
  • 4,234
1 vote
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rmsd between re-docked complex and co-crystallized complex

Welcome. The Protein-Ligand-complex is the complete protein with Ligand! If you only want to compare the two ligands, you can delete the rest of the proteins, or specify the input so only the ligand ...
Lucas's user avatar
  • 136
1 vote

Loop Pymol command get_area

Ok went back to this question having pymol within a hand's reach this time. Question is not really clear to me so I am posting a reasonable (to me) version of the ...
pippo1980's user avatar
  • 1,043
1 vote

Pymol: color spheres with different colors

Spheres So how PyMOL stores how it shows atoms is that each atom has a colour and a represention, which is a binary number telling what to show. Therefore the colour for ...
Matteo Ferla's user avatar
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1 vote

Selecting part of an extracted ligand

I know that structure way too well —SARS-COV-2 MPro. In PyMOL command line remove resn 02J or 010 or ...
Matteo Ferla's user avatar
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1 vote

Multiple input & output files?

You made the hardest work, you were not far to achieve what you wanted ;) This script.py should work after you made it executable (in a terminal type: ...
jeremy's user avatar
  • 143
1 vote

Modify how a script prints the output?

Let's simplify... cmd.distance(xx,xxx) accepts two selector strings and is fine with and state 1. And best of all if you select ...
Matteo Ferla's user avatar
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1 vote

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

To clarify, you are seeing reds and blues on the surface? If so, these are the sidechain oxygens and nitrogens. So you need to colour the whole residue not only the ...
Matteo Ferla's user avatar
  • 4,234
1 vote

Combine structures in the same session - PyMOL

Open the PyMOL session. Use the load command to load your PDB file(s): load file.pdb. Use the ...
jgreener's user avatar
  • 931
1 vote

Outputting crunchable list of HBonds from Pymol

Thanks a lot to all who commented/replied, the author of the scripts provided a response. It was down to a syntax change in PyMol of which I wasn't aware that caused my selection to come up empty.
LauraCZD's user avatar

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