[chimerax-users] outline the interface region in chimeraX

Thu Sep 9 16:47:42 PDT 2021

Hi, Tom,

Thank you so much for your suggestions! Very helpful!

Yes, I have the exactly same idea to make those outlined figs as described in your first email, but got the non-transparent background issue when exported those figs.

I’m using the photoshop function now to save the outlines with transparent background, but this does cost more time and effort.
So if the team could figure this issue out, that would be super cool.

Thank you very much!
And really appreciate the helpful suggestions and information from you and Elaine.

Best,
Bingchun

From: Tom Goddard <goddard at sonic.net>
Date: Thursday, September 9, 2021 at 7:39 PM
To: "Zhao, Bingchun (NIH/VRC) [F]" <bingchun.zhao at nih.gov>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] outline the interface region in chimeraX

Hi Bingchun,

  I tested that and also see that if a selection outline is shown then saving an image with transparent background does not give a transparent background.  I will make a bug report for that.  In the meantime you might need to use a photo editor and replace black with 100% transparency to work around this bug.

Tom

On Sep 9, 2021, at 2:56 PM, Zhao, Bingchun (NIH/VRC) [F] via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Hi, Elaine,

Thank you so much for your speedy reply!
This is really helpful!

One following question is, I found that when I select one area, the exported png fig is not with transparent background anymore, even I entered transparentBackground true in the commend line for saving.
Is there any solution for this? I mean how to keep those selection outline showing while I can still export png fig with transparent background?

Thank you very much!
Best,
Bingchun

From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
Reply-To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Date: Thursday, September 9, 2021 at 5:03 PM
To: "Zhao, Bingchun (NIH/VRC) [F]" <bingchun.zhao at nih.gov<mailto:bingchun.zhao at nih.gov>>
Cc: "chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>" <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Subject: Re: [chimerax-users] outline the interface region in chimeraX

Hi Bingchun,
There are two ways to show those patches in ChimeraX without using a separate drawing program.  One is just by coloring.  The only way I can think of to do an outline, however, is by selection.  You can change the color of the selection outline and its width, but you can only have one of those at a time, not several different outlines in different colors as shown in your example image.

I attach two example images, each with patch coloring on the left and selection outline on the right.  First is the default green selection and second is with a fatter white line obtained with command  "graphics selection color white width 4"

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection>
[cid:image001.png at 01D7A5B3.8C1CDDB0]

[cid:image002.png at 01D7A5B3.8C1CDDB0]

To make this example I opened 1zik, split into two models, deleted solvent.  I selected the interface atoms using:

contacts /a restrict /b sel true log true intersubmodel true

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>

...and then colored the chain B contacts and deselected them using:

color sel & /b yellow targ s
~sel #1.2

... and then used the "move picked models" mouse mode to rotate and translate the chains separately (they were in two different models because of the previous split command) so that the interfaces were toward the viewer.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 9, 2021, at 1:25 PM, Zhao, Bingchun (NIH/VRC) [F] via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Hi,

I wonder if there is a way to outline the interface region in ChimeraX like below:

<image001.png>

Previously, I did this in photoshop, but can we label the interface regions with those lines in ChimeraX?

Thank you very much!
Bingchun

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