I have created docked complex.pdbqt file using Autodock and I have uploaded that file in Pymol and visualized formed hydrogen bonds between ligand and protein, but the binding site residues of ligand can not labeled. How to highlight/label these binding site residues/ligand residues in Pymol?
Download UCSF's Chimera - molecular modelling software for visualization. https://www.cgl.ucsf.edu/chimera/
When you attempt to open your file it will not recognize the pdbqt extension, if you tell chimera to open it as a pdb file it will still work like normal. Chimera is super intuitive for finding residues that might be interacting with your ligand. You can select your ligand and actually search for anything that is forming a hydrogen bond with it. You can also search for any residue within a specific distance from a specific atom of your ligand (CNO or H specifically) or the whole ligand itself to find potential undetected / uncalculated bonds.
For a more detailed analysis of different types of interaction, you may use the Protein Ligand Interaction Profiles (PLIP), either the web server or the stand-alone program: https://projects.biotec.tu-dresden.de/plip-web/plip/help . As one of the results, it will generate a PyMOL .pse file visualizing the different types of interaction.
To create a named selection of contact atoms or contact residues, you can use the "within" command:
if "ligand" is the named selection representing your ligand, and "receptor" the named selection of your protein, you can get the contact atoms by:
select contact_atoms, receptor within 3.6 of ligand
Adjust the distance limits according to how stringent you want to be. 3.6Å for a structure without hydrogens would roughly get you direct VdW contacts, 5.0 Å solvent excluding contacts.
You can expand the selection to contact residues by:
select contact_residues, br. contact_atoms
You can then apply any display and coloring options to these selections, and list the content of the selection.
For more, see my tutorial slides at: Presentation Intermediate PyMOL
, on page 7 you see an example of selecting and coloring contact residues for a protein-protein interaction, protein-ligand interaction work just the same.
3D interaction with PyMol could be made easily if you have LigPlot+. After you have 2D interaction created by LigPlot+, call the PyMol from LigPlot+ and 3D interaction automatically build in PyMol.
Here is the link:
https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
Please open your docked pdb file in http://bioinformatics.org/pdbeditor/PDBEditor.jar and save it again in PDB format. This will solve your issue. The main problem you are facing is incorrect PDB file which is a source of error.
Hope it will work.
Try "discovery studio visualizer DSV" software for analyzing docking results to see the differents bonds between ligand and protein easily, it's a free software, also DSV provid many features for modeling and simulation like the 2D view and saving files in high resolution.
Discovery studio visualizer doesn't work on Intel graphics cards or does it? I'm having issues using it to visualize my output. Pdbqt file.
I need help with the visualization. Also, I cant find binding residues using pymol. I installed the autodock.py plugin but was told "could not initialize the autodock.py. what is the possible solution?
@Ojei Onyijen Discovery Studio Visualizer works well for me on Intel.
@Ojei Onyijen , to find interacting residues in PyMOL, you can use a distance criterion: If Lig is a named selection comprising your ligand, and Rec a selection of your receptor protein, select contact, Rec within 3.6 of Lig would select atoms that make direct VdW contact, select contact, Rec within 5.0 of Lig atoms that make solvent excluding contacts. If your structure contain explicit hydrogens, you would decrease the contact distances accordingly. To select the whole residues involved in contact, you would expand the selection by br., e.g. select contRes, br. contact see Presentation Intermediate PyMOL
SAMEE ULLAH
if I then wanted to export a list of the interacting residues to an output .txt file how could I do this?- Badges
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