Visually filtering out unstructured regions
Hi, I was looking for a way to filter out (hide) low scoring pLDDT regions of proteins so my models have less red "spaghetti strands" in my ribbon diagrams. I tried looking in the documentation for a command or pulldown option, but maybe missed it. Thanks in advance! David
The pLDDT is written to the b-factor column - so you can just use select by attribute to select a range, then delete or undisplay. Cheers Oli
On Apr 6, 2024, at 11:02 AM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I was looking for a way to filter out (hide) low scoring pLDDT regions of proteins so my models have less red "spaghetti strands" in my ribbon diagrams. I tried looking in the documentation for a command or pulldown option, but maybe missed it.
Thanks in advance!
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/
Command hide @@bfactor<50 ribbon Or use the AlphaFold Coloring panel using menu Tools / Structure Prediction / AlphaFold and press then press the Coloring button on the AlphaFold pane. The AlphaFold coloring GUI can color / show / hide / select low pLDDT regions https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring Tom
On Apr 6, 2024, at 11:00 AM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I was looking for a way to filter out (hide) low scoring pLDDT regions of proteins so my models have less red "spaghetti strands" in my ribbon diagrams. I tried looking in the documentation for a command or pulldown option, but maybe missed it.
Thanks in advance!
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/
Perfect. Thanks!!! David On Apr 6, 2024, at 4:21 PM, Tom Goddard <goddard@sonic.net> wrote: ◆ This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources. Command hide @@bfactor<50 ribbon Or use the AlphaFold Coloring panel using menu Tools / Structure Prediction / AlphaFold and press then press the Coloring button on the AlphaFold pane. The AlphaFold coloring GUI can color / show / hide / select low pLDDT regions https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring Tom On Apr 6, 2024, at 11:00 AM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi, I was looking for a way to filter out (hide) low scoring pLDDT regions of proteins so my models have less red "spaghetti strands" in my ribbon diagrams. I tried looking in the documentation for a command or pulldown option, but maybe missed it. Thanks in advance! 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/
participants (3)
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David S. Fay -
Oliver Clarke -
Tom Goddard