Filtering PAE Contacts–Interfaces
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
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
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 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html>: alphafold contacts atom-spec1 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> [ toAtoms atom-spec2 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> [ flip true | false ] [ distance d ] [ maxPae max-error ] [ palette <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> palette ] [ range <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> 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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Oops, my bad, sorry about that! I even read the page before posting the link, but somehow failed to notice the maxPae option. Elaine
On Jun 10, 2024, at 3:57 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
David S. Fay -
Elaine Meng -
Tom Goddard