Re: [Apbs-users] Net charge and contour level

[Nathan B. <ba...@cc...>]

Dear Dr. Deane --

Can you please clarify:  are you visualizing electrostatic potential
mapped onto a biomolecular surface or are you visualizing
electrostatic isocontours?  If it's the former, what surface are you
using for visualization -- solvent-accessible or molecular?

Thanks,

Nathan

On 10/17/07, Janet Deane <jan...@pa...> wrote:
> Dear apbs-users,
>
> We are using APBS tools in Pymol to compare the electrostatic surfaces
> of two related proteins. We are concerned about the correct way to
> display these so that the comparison is meaningful. Our question
> relates to the effect of the overall charge of the protein and the
> contours at which the electrostatic potential is displayed.
> Specifically, the calculated net charge of one of the proteins is -18
> and the other is -11 and if both are contoured between 4 and -4 one
> surface looks as though the charge density is exaggerated, i.e. there
> are very few patches without strong positive or negative charge.
>
> Thanks for any help,
> Janet
>
> --
> Dr Janet Deane
> Postdoctoral Researcher
> Sir William Dunn School of Pathology
> South Parks Rd
> University of Oxford OX1 3RE
> United Kingdom
> Phone: +44 1865 275385
> Email: jan...@pa...
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> _______________________________________________
> apbs-users mailing list
> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users
>


-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/