Hi Pierre,
Thanks for letting us know!  Hmmm, now I wonder if it is really supposed to say "lower in PAE" but I will doublecheck and it will be fixed soon.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco





> On Sep 6, 2024, at 4:55 AM, Bourguet,Pierre via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX support,
>
> First of all, thank you for developing & maintaining such an easy-to-use software. I am not trained as a structural biologist, but I looking at more and more structures thanks to alphafold. The journey is much nicer since I switched to ChimeraX!
>
> I have noticed the following inconsistency in the documentation.
> https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts
>
> "If one set of entities is higher-confidence (lower in pLDDT) than the other, it is usually best to specify them as the aligned set so that the coloring will show the error values of the lower-confidence set."
>
> My understanding is that it should say "(higher in pLDDT)".
>
> Hopefully that helps!
>
> Best,
> Pierre
> Pierre Bourguet
> Postdoc
>
> Gregor Mendel Institute of Molecular Plant Biology GmbH
> Dr. Bohr-Gasse 3, 1030 Vienna, Austria
> pierre.bourguet@gmi.oeaw.ac.at
> http://www.gmi.oeaw.ac.at
>
> <gmi_48f983b7-0679-4d21-99bc-bda376e5bf6b.png>
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