Hi Ye and Jared, there is also the "solvent_radius" setting:
PyMOL> set solvent_radius, 1.4 Cheers, Thomas On 14 Feb 2014, at 15:00, Sampson, Jared <[email protected]> wrote: > Hi Ye - > > The solvent excluded surface is the default surface representation in PyMOL. > (Solvent accessible surface can also be generated using `set surface_solvent, > on`.) View the surface with: > > show surface, myobj > > You can modify van der Waals radii like this: > > alter myobj, vdw=vdw*1.2 > rebuild > > You can also a selection or `all` instead of your object name. > > http://pymolwiki.org/index.php/Surface > http://pymolwiki.org/index.php/Surface_solvent > http://pymolwiki.org/index.php/Alter > > Cheers, > Jared > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > 550 First Avenue > New York, NY 10016 > 212-263-7898 > http://kong.med.nyu.edu/ > > > > On Feb 13, 2014, at 11:15 PM, ymei <[email protected]> wrote: > >> Hi all, >> >> Can anyone tell me how to generate the solvent exclusive surface with >> scaled (e.g. 1.2, 1.4, 1.6, etc) VDW radii for protein? >> I want to visualize the electrostatic potential on these surfaces, in >> order to get an idea how the potential changes from the protein to its >> vicinity. >> >> Thank you in advance. >> >> Ye -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
