Color AlphaFold PDB by B-Factor (pLDDT) in PyMol

Question

[Schmoho]

My understanding is, that AF puts the results of its predicted local distance difference test (pLDDT) in the B-factor column of a PDB file.

That would be the line from column 61-65, i.e. the last numeric field in my ATOMs:

ATOM   6018  CG  LEU A 773      58.102 -16.229 -52.934  1.00 61.72           C  

And indeded, these numbers correspond to what is listed as pLDDT in the .cif file.

However, when I run spectrum b, blue_white_red, my_protein, 0, 100 in PyMol, I get a uniform coloring. Running iterate my_protein, print(b) only prints zeroes.

So I think it is a pretty safe assumption that either PyMol fails at reading PDB format or I am fundamentally mistaken about something and I don't know what it is. I'd be so glad if someone could tell me which it is.

[Mensur Dlakic]

This should work. The only thing I can think about is that my_protein selection doesn't include the actual protein.

Do you get proper coloring by clicking on Color -> spectrum -> b-factors? What happens if you type spectrum b, blue_white_red, minimum=0, maximum=100 instead?

[Schmoho]

Consistently nothing happens, both via the UI and via the more explicit command. 'my_protein' is indeed selecting the correct protein, I double checked that. Interestingly, the cif-file from the same archive I got from the AF server colors correctly in PyMol.

I am using PyMol Version 3.0.0

[Mensur Dlakic]

Interestingly, the cif-file from the same archive I got from the AF server colors correctly in PyMol.

Then we are wasting time. Pretty sure nothing is wrong with PyMol, so something is off in that particular file.