Janet, This is really a question for the electrostatics experts, but it sounds reasonable to expect that a protein with a larger net charge would have more regions showing a strong negative potential. Given the large difference in net charge, a simple visual juxtaposition of potentials may not be all that informative.
Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:[email protected] "Not yet a PyMOL Subscriber, but want to support the project? Email [email protected] to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf > Of Janet Deane > Sent: Friday, October 19, 2007 2:59 AM > To: [email protected] > Subject: [PyMOL] APBS - Net charge and contour level > > Dear all, > > I have posted this message also to the APBS list but have not > yet had a response so if anyone here can help I'd be most grateful. > > 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. > Should the net charge be considered when choosing how to > contour the electrostatic surface? > > Cheers, > 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: [email protected] > > -------------------------------------------------------------- > ----------- > 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/ _______________________________________________ > PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users
