Fwd: Display of actual values of APBS electrostatic potential projected on protein surface
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: בעז שאנן bshaanan@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@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
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710
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@cgl.ucsf.edu wrote:
---------- Forwarded message ---------- From: בעז שאנן bshaanan@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@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
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@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@cgl.ucsf.edu wrote:
---------- Forwarded message ---------- From: בעז שאנן bshaanan@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@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
In my tests, if any other application has the focus then the surface values are reported in the status line in ChimeraX but not the chain info. The focus application does not need to be another ChimeraX and does not need to overlap the ChimeraX window. So that is a usable work-around.
Tom
On Sep 13, 2021, at 2:40 PM, Boaz Shaanan via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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@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 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@cgl.ucsf.edu wrote:
---------- Forwarded message ---------- From: בעז שאנן bshaanan@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@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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participants (3)
-
Boaz Shaanan -
Elaine Meng -
Tom Goddard