Using AlphaFold, I have predicted protein structure models and lDDT plot. Is there a way to color each model based on lDDT values using PyMOL? Thank you in advance.
This video demonstrates how you can open and color your PDB model with pLDDT scores.
https://youtu.be/WNYxRfd0TIE
Hi,
I think the simplest way to colour exactly how the (EBI AFDB) AlphaFold colouring scheme is to download and then in your pymol session to run this Bob Schiffrin's pymol script- https://github.com/BobSchiffrin/pymol_scripts
colour_af_plddt.py.
Hello there,
If you have an AlphaFold-generated model, the pLDDT values are stored as beta factors in the pdb file (https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/dealing-with-coordinates).
If you load said pdb file into Pymol, you can easily color the model by pLDDT value by writing in the command-line "spectrum b, red blue" (to color from red-worst to blue-best)
I also recommend the PyMOL plugin https://github.com/cbalbin-bio/pymol-color-alphafold
You can run it from the PyMOL prompt as it is indicated in github or you can install the plugin coloraf.py in PyMOL from the same address.
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