## [Apbs-users] Comparing potentials

 [Apbs-users] Comparing potentials From: Sigrid Gåseidnes - 2008-06-08 20:43:40 Attachments: Message as HTML ```Dear all, We have just started doing electrostatic calculations with APBS. The problem we want to solve is to compare the electrostatic surface potential of a chitinase (1e15) with a 9 fold mutant of the same enzyme. When we look at the individual electrostatic maps in PyMol we can see differences between the two, but we would like to quantify and map the differences more precisely. So far we have tried to compare the wt and mutant potentials by subtracting the mutant grid values from the corresponding wt value at the same grid points. We then visualize the result grid in PyMol to highlight the areas of difference (grid points with small differences between them are set to zero). Is this a possible solution to our problem? If not, any suggestions of other ways to proceed? Yours sincerely, Sigrid Gåseidnes, Post doc Institute of Chemistry, Biotechnology and Foodsciences Norwegian University of Life Sciences ```

 [Apbs-users] Comparing potentials From: Sigrid Gåseidnes - 2008-06-08 20:43:40 Attachments: Message as HTML ```Dear all, We have just started doing electrostatic calculations with APBS. The problem we want to solve is to compare the electrostatic surface potential of a chitinase (1e15) with a 9 fold mutant of the same enzyme. When we look at the individual electrostatic maps in PyMol we can see differences between the two, but we would like to quantify and map the differences more precisely. So far we have tried to compare the wt and mutant potentials by subtracting the mutant grid values from the corresponding wt value at the same grid points. We then visualize the result grid in PyMol to highlight the areas of difference (grid points with small differences between them are set to zero). Is this a possible solution to our problem? If not, any suggestions of other ways to proceed? Yours sincerely, Sigrid Gåseidnes, Post doc Institute of Chemistry, Biotechnology and Foodsciences Norwegian University of Life Sciences ```
 Re: [Apbs-users] Comparing potentials From: Nathan Baker - 2008-06-10 12:21:24 ```Hello -- This sounds like a very reasonable plan for comparing potentials. APBS also provides tools for such comparison of aligned proteins (see apbs/tools/mesh/similarity); note that this just provides a numerical metric of similarity rather than visualization. Finally, Rebecca Wade's group (EML Heidelberg) has a number of tools that might be useful for your analysis, including MolSurfer and webPIPSA. Good luck, Nathan On Jun 8, 2008, at 4:43 PM, Sigrid Gåseidnes wrote: > Dear all, > We have just started doing electrostatic calculations with APBS. The > problem we want to solve is to compare the electrostatic surface > potential of a chitinase (1e15) with a 9 fold mutant of the same > enzyme. When we look at the individual electrostatic maps in PyMol > we can see differences between the two, but we would like to > quantify and map the differences more precisely. > > So far we have tried to compare the wt and mutant potentials by > subtracting the mutant grid values from the corresponding wt value > at the same grid points. We then visualize the result grid in PyMol > to highlight the areas of difference (grid points with small > differences between them are set to zero). Is this a possible > solution to our problem? If not, any suggestions of other ways to > proceed? > > Yours sincerely, > > Sigrid Gåseidnes, Post doc > Institute of Chemistry, Biotechnology and Foodsciences > Norwegian University of Life Sciences > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php_______________________________________________ > apbs-users mailing list > apbs-users@... > 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/ -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ```