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amjjbonvin committed Nov 23, 2024
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Expand Up @@ -738,13 +738,13 @@ Examine the various models. How does the orientation of the antigen differ betwe
</summary>

When looking at the structures generated by AlphaFold in PyMOL, the pLDDT is encoded as the B-factor. <br>
To color the model according to the pLDDT type in PyMOL:
To color the model according to the pLDDT type in PyMOL:<br>
<br>
<a class="prompt prompt-pymol">
spectrum b
</a>

**Note** that the scale in the B-factor field is the inverse of the color coding in the PAE plots:
<br>
<b>Note</b> that the scale in the B-factor field is the inverse of the color coding in the PAE plots:
i.e. red mean reliable (high pLDDT) and blue unreliable (low pLDDT)). If you want to have the inverse coloring
you can use a PyMol plugin, e.g. as described <a href="https://github.com/cbalbin-bio/pymol-color-alphafold" target="_blank"><b><i>here</i></b>.</a>
</details>
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