Enquiry regarding electrostatics calculations of outersurface
Dear all Chimera users, Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script. However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms. My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them? I would greatly appreciate your help. Best Regards, Jian Chen
Hi Jian, The surfval.py script already gives you the values at the molecular surface vertices. Of course there are many more surface vertices than atoms. I.e. show the surface as mesh, you can see how many vertices it has. If you just want to get the value at some specific atom center, then use "Values at Atom Positions." However, this is not really meaningful, as there will be a spike in the potential if it is at the same location as a charge used to calculate that potential. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.ht...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 14, 2020, at 9:32 PM, Jian Chen <chenj15@fudan.edu.cn> wrote:
Dear all Chimera users , Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script.
However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms.
My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them?
I would greatly appreciate your help.
Best Regards,
Jian Chen
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine, Thank you very much for your help. There are so many vertices on the surface, and I want to caculate the charge values and the area of the positive/negtive charge patches. So my question is, how can we distinguish the coordinates of patches from others? Do vertices nearby have an overlap area according to the calculation using APBS? Thank you again for your help! Best Regards, Jian Chen
-----原始邮件----- 发件人: "Elaine Meng" <meng@cgl.ucsf.edu> 发送时间: 2020-04-16 00:36:12 (星期四) 收件人: "Jian Chen" <chenj15@fudan.edu.cn> 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] Enquiry regarding electrostatics calculations of outersurface
Hi Jian, The surfval.py script already gives you the values at the molecular surface vertices. Of course there are many more surface vertices than atoms. I.e. show the surface as mesh, you can see how many vertices it has.
If you just want to get the value at some specific atom center, then use "Values at Atom Positions." However, this is not really meaningful, as there will be a spike in the potential if it is at the same location as a charge used to calculate that potential. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.ht...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 14, 2020, at 9:32 PM, Jian Chen <chenj15@fudan.edu.cn> wrote:
Dear all Chimera users , Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script.
However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms.
My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them?
I would greatly appreciate your help.
Best Regards,
Jian Chen
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Jian Chen Chenj15@fudan.edu.cn Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose Throat Hospital of Fndan University Address: No.83Fenyang Road, Xuhui District, Shanghai, P.R.China
Hi Jian, (1) it is not charge, it is electrostatic potential (ESP) ... to learn the difference, can read papers about these calculations (e.g. APBS), or various information online such as this: <https://www.reed.edu/chemistry/ROCO/Potential/electrostatic_potential.html> (2) in surfval.py I see this line f.write('# %8s %10s %10s %10s %10s\n' % ('x', 'y', 'z', 'area', 'value')) ...so it writes the xyz coordinates, area, and value of each vertex. It is up to you to do further calculations using these values, if you want... However, electrostatic surface coloring is generally meant for visual analysis, not quantitative, because much of the information is in the spatial distribution of the ESP and the shape of the surface pockets. I would not recommend trying to boil that down to some "positive area" and "negative area" values; that loses most of the information, and you'd have to choose arbitrary cutoff values to distinguish what is near-neutral vs. positive vs. negative. To compare ESP between different (yet similar) structures, you might be interested in this web server PIPSA: <https://pipsa.h-its.org/pipsa/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 15, 2020, at 7:47 PM, Jian Chen <chenj15@fudan.edu.cn> wrote:
Dear Elaine,
Thank you very much for your help.
There are so many vertices on the surface, and I want to caculate the charge values and the area of the positive/negtive charge patches. So my question is, how can we distinguish the coordinates of patches from others? Do vertices nearby have an overlap area according to the calculation using APBS?
Thank you again for your help!
Best Regards,
Jian Chen
-----原始邮件----- 发件人: "Elaine Meng" <meng@cgl.ucsf.edu> 发送时间: 2020-04-16 00:36:12 (星期四) 收件人: "Jian Chen" <chenj15@fudan.edu.cn> 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] Enquiry regarding electrostatics calculations of outersurface
Hi Jian, The surfval.py script already gives you the values at the molecular surface vertices. Of course there are many more surface vertices than atoms. I.e. show the surface as mesh, you can see how many vertices it has.
If you just want to get the value at some specific atom center, then use "Values at Atom Positions." However, this is not really meaningful, as there will be a spike in the potential if it is at the same location as a charge used to calculate that potential. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.ht...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 14, 2020, at 9:32 PM, Jian Chen <chenj15@fudan.edu.cn> wrote:
Dear all Chimera users , Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script.
However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms.
My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them?
I would greatly appreciate your help.
Best Regards,
Jian Chen
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Jian Chen Chenj15@fudan.edu.cn Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose Throat Hospital of Fndan University Address: No.83Fenyang Road, Xuhui District, Shanghai, P.R.China
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Jian Chen