Jed, Yes, essentially. Surface_cavity_mode will help along with findSurfaceResidues.py. If you want to see only internal cavities, but show the voids as surfaces then start with:
set surface_cavity_mode, 1 Next, defining what is a "surface" residue depends on the surface area exposed to solvent. The default for findSurfaceResidues is 2.5 A**2. If you want a real tight definition, where nearly any exposed surface will qualify, then try something like: findSurfaceResidues prot, 0.5 (Also, see "help findSurfaceResidues" for more help.) Here's a few examples combining these two techniques: load $TUT/1hpv.pdb remove het as surface # normal surface set surface_cavity_mode, 1 # show only cavities Now, purge those residues closer to the surface, findSurfaceResidues 1hpv, 2.5 # select AAs w/2.5 A**2 surface area flag ignore exposed_XYZ1 # remove surface atoms rebuild findSurfaceResidues 1hpv, 0.5 # select AAs w/0.5 A**2 surface area flag ignore exposed_XYZ2 # remove surface atoms rebuild So, while 2.5 A**2 is the std. definition, play with it and see what you get. Good luck, -- Jason On Wed, Jan 13, 2010 at 2:09 PM, Jed Goldstone <[email protected]> wrote: > Jason- > > Quick question regarding this - I would like to do the inverse - that is, > show only the surface of interior pockets. So: > > fetch 2hi4 > run findSurfaceResidues.py > findSurfaceResidues (1phv), 0.5 > flag ignore, exposed_RESULT > as surface, 2hi4 > > Yes? > > Jed > > Jason Vertrees wrote: >> >> Hugues, >> >> Here's a tricky way to do it: >> >> Download and run "findSurfacerResidues" >> (http://pymolwiki.org/index.php/FindSurfaceResidues) and run it on >> your protein. The resultant selection contains surface residues. >> Next, just set the "flag" on all those that are not returned and show >> that as surface. >> >> Example: >> >> fetch 1hpv >> run findSurfaceResidues.py >> # this function returns a selection called "EXPOSED_XYZ" where XYZ is >> some random integer >> findSurfaceResidues (1phv), 0.5 >> >> flag ignore, not exposed_RESULT >> as surface, 1hpv >> >> Let me know if that works. By the way, you might need to "rebuild" >> after setting the flag. >> >> Hope this helps, >> >> -- Jason >> >> On Tue, Jan 12, 2010 at 11:51 AM, Hugues Nury <[email protected]> >> wrote: >> >>> >>> Dear Pymolers, >>> >>> Do you know if there is a way to display only the outer surface of a >>> protein without its buried pockets ? I've noticed that >>> set surface_cavity_mode, 1 >>> does the opposite, ie display 'inner' surfaces only, but I haven't >>> found the setting for the other way round. >>> >>> Thanks for you help, >>> Hugues >>> >>> -- >>> Hugues Nury >>> Postdoctoral fellow, Dynamique Structurale des Macromolécules >>> Institut Pasteur, Paris, France >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast and >>> easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >>> >> >> >> >> > > -- > ------------------------ > Jed Goldstone > Research Specialist > Woods Hole Oceanographic Institution > Redfield 3-52 MS#32 > Woods Hole, MA 02543 > http://www.whoi.edu/hpb/Site.do?id=481 > Phone: 508-289-4823 > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
