Values on electrostatic map at mouse locations (in surface-colour-options)
Hi, I'm seeing some weird values when I use this option, for example high +ve value when touching a very red area or -ve on a very blue area ( I use 3 colours scheme). I'm running linux alpha version v. 1.13 (build 41653) from 5 Jan 2018. The electrostatic potential was calculated in delphi. I have a vague recollection that this feature behaved more reasonably in the past when I used it (I could of course be wrong). Thanks for your help. 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 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
Hi Boaz, For the most reasonable values, make sure that when you color by electrostatic potential, you use the “Surface offset” (default 1.4 Angstroms) to color the solvent-excluded surface by values measured some distance outside the surface. The default distance is a “water” probe radius, approximating the location of the solvent-accessible surface. The (displayed) solvent-excluded surface is about that much closer to the atomic centers, the locations of the point charges used to calculate the ESP, than the solvent-accessible surface (not displayed). Another potential foible is using some all-atom charge model on a structure that doesn’t have any hydrogens, so the whole thing is overwhelmingly negative. However, if you are also seeing large magnitudes on positive regions, that probably isn’t an issue for you. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2018, at 3:26 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, I'm seeing some weird values when I use this option, for example high +ve value when touching a very red area or -ve on a very blue area ( I use 3 colours scheme). I'm running linux alpha version v. 1.13 (build 41653) from 5 Jan 2018. The electrostatic potential was calculated in delphi. I have a vague recollection that this feature behaved more reasonably in the past when I used it (I could of course be wrong). Thanks for your help. Boaz
Other than ESP calculation parameters, my only other idea is to make sure your map is correctly aligned with the surface. If the map is rotated or translated relative to the displayed surface, that would be another way that the surface vertices could come too close to the near-singularities at atom centers (point charges) within the map. Best, Elaine
On Feb 4, 2018, at 12:57 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi Elaine, Thanks a lot for your prompt reply and suggestions. I use the default surface offset of 1.4 A. I'll look into your other suggestions on the calculation of the potenial. The protein is halophilic and hence extremely negative overall with positive patch in the putative dna binding site. Playing with the calculation params is an important factor as you pointed out.
Best regards, Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University
On Sun, Feb 4, 2018 at 8:36 PM +0200, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Boaz, For the most reasonable values, make sure that when you color by electrostatic potential, you use the “Surface offset” (default 1.4 Angstroms) to color the solvent-excluded surface by values measured some distance outside the surface. The default distance is a “water” probe radius, approximating the location of the solvent-accessible surface.
The (displayed) solvent-excluded surface is about that much closer to the atomic centers, the locations of the point charges used to calculate the ESP, than the solvent-accessible surface (not displayed).
Another potential foible is using some all-atom charge model on a structure that doesn’t have any hydrogens, so the whole thing is overwhelmingly negative. However, if you are also seeing large magnitudes on positive regions, that probably isn’t an issue for you. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2018, at 3:26 PM, Boaz Shaanan wrote:
Hi, I'm seeing some weird values when I use this option, for example high +ve value when touching a very red area or -ve on a very blue area ( I use 3 colours scheme). I'm running linux alpha version v. 1.13 (build 41653) from 5 Jan 2018. The electrostatic potential was calculated in delphi. I have a vague recollection that this feature behaved more reasonably in the past when I used it (I could of course be wrong). Thanks for your help. Boaz
Hi Boaz, It’s more a matter of making sure you don’t do anything to un-align them. :-) Basically, show the surface using the same atomic coordinates as used to calculate the ESP, and do not move the map model separately from the atomic model (e.g. by unchecking the “A” in the Model Panel to freeze one model in place while moving the other one around). Elaine
On Feb 5, 2018, at 10:11 AM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Thanks Elaine, but how can I ensure that the map is indeed aligned with the surface? Is it something I have specify in Delphi? Maybe move the molecule to the origin prior to calculating esp? I'd appreciate advice on that if possible. Thanks, Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University
On Mon, Feb 5, 2018 at 8:05 PM +0200, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Other than ESP calculation parameters, my only other idea is to make sure your map is correctly aligned with the surface. If the map is rotated or translated relative to the displayed surface, that would be another way that the surface vertices could come too close to the near-singularities at atom centers (point charges) within the map. Best, Elaine
On Feb 4, 2018, at 12:57 PM, Boaz Shaanan wrote:
Hi Elaine, Thanks a lot for your prompt reply and suggestions. I use the default surface offset of 1.4 A. I'll look into your other suggestions on the calculation of the potenial. The protein is halophilic and hence extremely negative overall with positive patch in the putative dna binding site. Playing with the calculation params is an important factor as you pointed out.
Best regards, Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University
On Sun, Feb 4, 2018 at 8:36 PM +0200, "Elaine Meng" wrote:
Hi Boaz, For the most reasonable values, make sure that when you color by electrostatic potential, you use the “Surface offset” (default 1.4 Angstroms) to color the solvent-excluded surface by values measured some distance outside the surface. The default distance is a “water” probe radius, approximating the location of the solvent-accessible surface.
The (displayed) solvent-excluded surface is about that much closer to the atomic centers, the locations of the point charges used to calculate the ESP, than the solvent-accessible surface (not displayed).
Another potential foible is using some all-atom charge model on a structure that doesn’t have any hydrogens, so the whole thing is overwhelmingly negative. However, if you are also seeing large magnitudes on positive regions, that probably isn’t an issue for you. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2018, at 3:26 PM, Boaz Shaanan wrote:
Hi, I'm seeing some weird values when I use this option, for example high +ve value when touching a very red area or -ve on a very blue area ( I use 3 colours scheme). I'm running linux alpha version v. 1.13 (build 41653) from 5 Jan 2018. The electrostatic potential was calculated in delphi. I have a vague recollection that this feature behaved more reasonably in the past when I used it (I could of course be wrong). Thanks for your help. Boaz
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No worries at all, it happens to the best of us! I didn’t spend much time, and I’m glad it’s resolved. :-) Elaine
On Feb 5, 2018, at 2:08 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi Elaine,
Shame on me! I looked at the last of the four numbers that appear when you ask to report the potential value at the mouse, which is of course the Z coordinate of the point instead of looking at the first number. It's only when I re-calculated a new map and surface that it finally dawned on me how stupid I was. I am so embarrassed. I hope you didn't spend too much energy trying to figure out what went wrong with my esp-surface relations.
I am very sorry.
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 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 5, 2018 8:14 PM To: בעז שאנן Cc: UCSF Chimera Mailing List Subject: Re: [Chimera-users] Values on electrostatic map at mouse locations (in surface-colour-options)
Hi Boaz, It’s more a matter of making sure you don’t do anything to un-align them. :-)
Basically, show the surface using the same atomic coordinates as used to calculate the ESP, and do not move the map model separately from the atomic model (e.g. by unchecking the “A” in the Model Panel to freeze one model in place while moving the other one around). Elaine
On Feb 5, 2018, at 10:11 AM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Thanks Elaine, but how can I ensure that the map is indeed aligned with the surface? Is it something I have specify in Delphi? Maybe move the molecule to the origin prior to calculating esp? I'd appreciate advice on that if possible. Thanks, Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University
On Mon, Feb 5, 2018 at 8:05 PM +0200, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Other than ESP calculation parameters, my only other idea is to make sure your map is correctly aligned with the surface. If the map is rotated or translated relative to the displayed surface, that would be another way that the surface vertices could come too close to the near-singularities at atom centers (point charges) within the map. Best, Elaine
On Feb 4, 2018, at 12:57 PM, Boaz Shaanan wrote:
Hi Elaine, Thanks a lot for your prompt reply and suggestions. I use the default surface offset of 1.4 A. I'll look into your other suggestions on the calculation of the potenial. The protein is halophilic and hence extremely negative overall with positive patch in the putative dna binding site. Playing with the calculation params is an important factor as you pointed out.
Best regards, Boaz
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University
On Sun, Feb 4, 2018 at 8:36 PM +0200, "Elaine Meng" wrote:
Hi Boaz, For the most reasonable values, make sure that when you color by electrostatic potential, you use the “Surface offset” (default 1.4 Angstroms) to color the solvent-excluded surface by values measured some distance outside the surface. The default distance is a “water” probe radius, approximating the location of the solvent-accessible surface.
The (displayed) solvent-excluded surface is about that much closer to the atomic centers, the locations of the point charges used to calculate the ESP, than the solvent-accessible surface (not displayed).
Another potential foible is using some all-atom charge model on a structure that doesn’t have any hydrogens, so the whole thing is overwhelmingly negative. However, if you are also seeing large magnitudes on positive regions, that probably isn’t an issue for you. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2018, at 3:26 PM, Boaz Shaanan wrote:
Hi, I'm seeing some weird values when I use this option, for example high +ve value when touching a very red area or -ve on a very blue area ( I use 3 colours scheme). I'm running linux alpha version v. 1.13 (build 41653) from 5 Jan 2018. The electrostatic potential was calculated in delphi. I have a vague recollection that this feature behaved more reasonably in the past when I used it (I could of course be wrong). Thanks for your help. Boaz
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Elaine Meng