There is only one selection outline in ChimeraX so you cannot show different color outlines directly in ChimeraX using the selection outline. Here are a couple ideas. You could select all your sites and make one outline around all of them in green
and then in Photoshop change the color of parts of the outline to the appropriate colors. Another idea is you can select each patch and make its outline in the correct color and then just save that outline but not the surface. To show just the outline and
not the surface you would make the surface 100% transparent and hide atoms
transparency 100
hide atoms
save outline1.png transparentBackground true.
Save each outline as a separate image and then layer them on top of your surface in Photoshop. A problem with both of these methods is that your patches border each other so the outlines will overlap. In fact the selection outline extends outward when
you make it thicker (ChimeraX avoids covering the patch with the outline). So two adjacent patches with different outlines are going to draw the outlines intersecting and crossing each other where they adjoin each other. Making the outlines extend inward
could be done in Photoshop by fattening the individual layer outlines. This gets into a lot of hand work.
Tom
On Dec 7, 2023, at 1:15 PM, Andre Leon <aleon@scripps.edu> wrote:
Hello Tom,
Thank you for the response! I'm guessing the answer to my next question is no, but I was wondering if there's a way to create these selection outlines around multiple regions to create figures similar to the one below, highlighting all the major antigenic sites on influenza HA. That way I can simultaneously outline the epitopes and also color the figure by sequence conservation as opposed to doing one or the other. If that's not possible, than I will pseudo outline in Illustrator or Photoshop, but it would be ideal to be able to specifically highlight the exact residues using ChimeraX.
Again, thank you so much for your rapid response!
From: Tom Goddard <goddard@sonic.net>
Sent: Thursday, December 7, 2023 12:25 PM
To: Andre Leon <aleon@scripps.edu>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Following Up on Drawing OutlinesHi André,
Making a thick colored outline around an epitope on a protein surface is easier in ChimeraX using thick selection outlines. The link you mentioned from 2014 is from our old program Chimera which could only draw thin 1 pixel wide outlines. Here is an example in ChimeraX where I make a thick (10 pixel wide) red outline around some residues.
open 2x7rhide ~/C atomssurface /Cselect /C:670-681graphics selection color red width 10
Tom
On Dec 7, 2023, at 10:53 AM, Andre Leon via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Chimerax,
I was wondering if there has been any progress on making outlines of specific epitopes in ChimeraX since this thread back in 2014? Thank you in advance.
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