Firstly, I think in Pymol there is no true electrostatic potential calculator, but only a "charge-smoothed" surface presentation ( http://www.pymolwiki.org/index.php/Protein_contact_potential).
So, If you want to calculate the real electrostatic potential in Pymol (by Possion-Boltzman method), you have to install a plugin such as APBS or Delphi. Personally, I prefer Delphi, because there is a good and simple tutorial written by James Stroud from USC ( http://structure.usc.edu/howto/delphi-surface-pymol.html). And you also can read the man page of Delphi where describe the details how it works ( http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi). On Thu, May 26, 2011 at 12:51 PM, Tim Gruene <[email protected]>wrote: > Dear Maher, > > as far as I know pymol uses the APBS (http://www.poissonboltzmann.org) for > the > calculations and your question is answered in the FAQ: > > http://www.poissonboltzmann.org/apbs/frequently-asked-questions/what-are-the-units-of-electrostatic-potential > (kT/e) > > I don't know if this also answers your second question, but you could let > us > know in case it does. > > Tim > > On Wed, May 25, 2011 at 03:58:17PM -0700, Maher Alayyoubi wrote: > > Hi everyone, I have two questions: > > > > 1- Does anybody know what are the units on the display ruler after you > > calculate the vaccum electrostatics using pymol? > > > > 2- What are the default kT/e values used by pymol? > > > > Thank you, > > > > > > > > > > Maher > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > > iD8DBQFN3jDOUxlJ7aRr7hoRAuONAJ9/PlFL6WgLhiw44GrofkSibUw8IgCfRQxh > YhReBu+gIxwpBm/7PHQwW4w= > =dLaZ > -----END PGP SIGNATURE----- > > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
