[chimerax-users] Display of actual values of APBS electrostatic potential projected on protein surface

[Boaz Shaanan]

Hi Elaine,
Thanks for your prompt reply and suggestion to improve the feature. I'm just beginning to enjoy the Chimerax option of showing surface of any buried part of the protein, (It's great!) so the idea of specific potential values in buried places came to mind. I'll play with it as it is now ( I will also try opening another window)  and wait for the feature implemenation you suggested.

Best regards,
Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On 13 Sep 2021 15:55, Elaine Meng <meng at cgl.ucsf.edu> wrote:
Hi Boaz,
Yes, it's your [semi]-lucky day!  In the Surface Color tool in the menu under Tools... Depiction, the Options include

• Report value at mouse position – whether mouseover (when mouse focus is in the graphics window) should report the data value for that surface vertex in the status line

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>

I say "semi," however, because currently it is very annoying to use, as you need to very quickly move the mouse away from the surface afterward or else the status line will switch to showing the chain information instead, e.g. "chain L: low density lipoprotein receptor variant".  Strangely, when I started a second ChimeraX window (but didn't do anything else with that second instance other than leave it on top with the mouse focus in it, slightly overlapping the first window), this problem stopped, and the original window's mouseovers would stably show the value in the status line.  That might be something weird specific to my laptop, however.

Anyway, I will make a ticket for the annoying behavior mentioned above and put you on the notification list.  Sorry about that!

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 13, 2021, at 1:01 PM, Boaz Shaanan via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> ---------- Forwarded message ----------
> From: בעז שאנן <bshaanan at bgu.ac.il>
> Date: 9 Sep 2021 17:39
> Subject: Display of actual values of APBS electrostatic potential projected on protein surface
> To: ChimeraX-users-request at cgl.ucsf.edu
> Cc:
>
> Hi,
> Is there a way in Chimerax to know the actual APBS electrostatic potential values in various points on the surface?
> Is there such feature already in Chimerax that I missed? Such feature is essential (I think) to monitor subtle changes in surface potential following mutations or other variations (pH, salt concentration etc.). If it's not there yet, could you please add it to the (enormous, I guess) to-do list?
>
>  In Chimera this is done by moving  the cursor to the various points of interest, a feature that I found most useful (and helpful in convincing color blind referees 😉).
>
> Cheers,
>
>                Boaz

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