Hi David,

  The "alphafold contacts" command has a maxPae option.

    alphafold contacts /A to /B distance 5 maxPae 10

Remember the low PAE values are good confidence (they are distances in Angstroms), so it is the high PAE values you probably want to filter out, not the low ones to see where the interface is confident.  Documentation in the ChimeraX user guide

    https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts

    Usage: alphafold contacts  atom-spec1  [ toAtoms  atom-spec2  [ flip  true | false ] [ distance  d ] [ maxPae  max-error ] [ palette  palette ] [ range  low,high | full ] [ radius  r ] [ dashes  N ] [ name  model-name ] [ replace  true | false ] [ outputFile  pae-file ]


  Tom



On Jun 10, 2024, at 3:25 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi David,
(1) The range option only affects the palette (how the colors are mapped to PAE values), not which lines are shown by "alphafold contacts":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts>

(2) The coloring of the lines is based on PAE values (pairwise residue-residue values), not pLDDT which is per individual residue and typically used for the coloring of the ribbons.

(3) Which lines are shown is controlled by the distance option of "alphafold contacts" and I don't know of a way to limit them by PAE value with the "alphafold contacts" command.  Maybe these pseudobonds have an associated PAE-value attribute which could be used to hide and show some of them, but I don't know if that is so, or what it would be named.  Maybe the others on the team can comment about this?

I hope this clarifies things,
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 Jun 10, 2024, at 3:05 PM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Was attempting (unsuccessfully) to filter out lower scoring (red/yellow) PAE contacts when viewing interaction interfaces between two or more proteins.

I normally use a command such as: alphafold contacts /A to /B distance 5

But then I’d like to limit what I see to regions with high pLDDT scores (blue lines). I tried playing with range, but keep getting errors.

Thanks!

David


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