[chimerax-users] Identifying residues based on PAE plot?

[Tom Goddard]

Hi Jan,

  Those are good suggestions.  I plan to have the PAE plot show you the residue numbers when you hover the mouse.  But I agree that making a drag box on the plot do a selection of residues could be useful.  I made it do coloring like the AlphaFold database web pages which show these plots because I think it was visually clearer.  When it does the coloring, it replaces the entire coloring, including the residues outside the box you dragged.  Maybe I can add an option to the plot to select instead of color.  I find the plot button that colors domains does a nice job of showing the different regions where AlphaFold is confident.  Gerard Kleywegt suggested also showing those same colors in the plot itself so the correspondence and interactions between the domains on the plot could easily be seen.  I've made feature requests for these ideas.

	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6724
	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6725

  There are lot of other PAE improvements I am looking into, like putting in dividing lines on the plot between proteins for multimer predictions, zooming the plots, or coloring by confidence relative to residues chosen on the structure.

  Having a linear plot of pLDDT (predicted local distance difference test) per-residue scores could be nice.  But I am a bit unclear on how it would be used.  You already see the pLDDT coloring on the structure which makes those red unstructured regions stand out.  In the ChimeraX AlphaFold tool (menu Tools / Structure Prediction / AlphaFold) there is a Coloring button that shows a panel where you can select all residues below a given pLDDT (confidence) score.  So you can then delete them, or change their style, or do whatever you want with those selected residues.

  Here's a bit of info on the current ChimeraX PAE capabilities

	https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html

  Tom




> On Apr 27, 2022, at 3:08 AM, mailman-bounces--- via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> From: "Jan Gebauer" <jan.gebauer at uni-koeln.de <mailto:jan.gebauer at uni-koeln.de>>
> Subject: Identifying residues based on PAE plot?
> Date: April 27, 2022 at 3:04:30 AM PDT
> To: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu>>
> Reply-To: "Jan Gebauer" <jan.gebauer at uni-koeln.de <mailto:jan.gebauer at uni-koeln.de>>
> 
> 
> Hi everyone,
> 
> love the "new" work in the dailys for ChimeraX and visualising the PAE and pLDTT scores. As I calculate my AF structures on my own, this helps a lot to analyses the structures.
> 
> I have one question/suggestion however: If I select a region in the PAE plot, it gets coloured in the the "3D-view", however, I found no way to actually get the residues number or a proper selection for the coloured residues. Is there a way? I'd like to colour multiple selections differently...
> Another nice feature would be a pLDTT plot, as this enables easier detection of unordered stretches...
> 
> As always: Many thanks for all the good work!
> 
> Best
> Jan
> 
> --
> Dr. Jan Gebauer | 💎 Head of C2f |🔬 Member of AG Prof. Baumann
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