[Chimera-users] Enquiry regarding electrostatics calculations of outersurface

[Jian Chen]

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 at cgl.ucsf.edu>
> 发送时间: 2020-04-16 00:36:12 (星期四)
> 收件人: "Jian Chen" <chenj15 at fudan.edu.cn>
> 抄送: chimera-users at 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.html>
> 
> 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 at 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
> > 
> > 
> > 
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--
Jian Chen 
Chenj15 at 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