Hi Ben, Michael's advice is pretty solid--I would start there.
Having said that, PyMOL does have a few tricks to allow you to find and highlight such pockets, but it could get tricky. # fetch a protein with a buried ligand fetch 1qkt, async=0 # pull out the ligand to its own object extract ligand, org # make a real selection select lig, org # set the selection set surface_carve_selection, lig # set the cutoff; hide surface >4.5 Ang from lig set surface_carve_cutoff, 5.5 # let PyMOL consider surfacing everything flag ignore, none # show surface (using above constraints) show surface # hide the ligand surface hide surface, lig # set up the view/reps set surface_color, 0x778899 set transparency, 0.5 orient org zoom org, 5 set two_sided_lighting rebuild ray See: * -- http://www.pymolwiki.org/index.php/Surface_carve_selection * -- http://www.pymolwiki.org/index.php/Surface_carve_cutoff Hope this helps. Cheers, -- Jason On Fri, May 20, 2011 at 7:38 PM, Michael Lerner <mgler...@gmail.com> wrote: > The last time I tried to do something similar, I found HOLLOW > (http://hollow.sourceforge.net/) to be very useful. There's a nice tutorial > for showing a binding site, rather than an interior cavity, > here: http://hollow.sourceforge.net/binding.html . > Cheers, > -Michael > > On Fri, May 20, 2011 at 7:11 PM, Ben Roberts <b...@roberts.geek.nz> wrote: >> >> Hi list, >> >> I'm trying to use PyMOL to construct an image of the total contiguous >> contact >> surface that starts at a particular place on the surface of a protein, >> without >> all the visual distraction and clutter that comes from other regions of >> the >> protein surface (not to mention internal cavities). >> >> I started by rendering up the whole protein as "Contact surface" with >> "Cavities and pockets only" shown. Unfortunately, this displays a large >> number >> of bubbles, some of which, despite being far away in space from the region >> of >> interest, manage to effectively obscure bits and pieces of it. >> >> So my next thought was to try removing the extraneous bits, however, I >> can't >> seem to select atoms in surface view; I have to display everything as >> lines or >> similar. Removing things that way gets very unwieldy, not least because of >> all >> the atoms that don't contribute anything to the surface but appear in >> front >> of, behind, or otherwise near to the atoms that do so. >> >> A third option I tried was to build the surface up, starting from the >> known >> points of interest, but this too is painstaking because of the need to >> guess >> where I should next expand the selection to in order to fill in the gaps. >> >> A remaining method of getting only the cavity of interest would, I guess, >> be >> to create a selection consisting only of those atoms that contribute >> something >> to the currently rendered surface (in this case, cavities and voids). I >> could >> then render those as spheres or something and hide unwanted contributors. >> Is >> there a way of specifying such a selection? Alternatively, is there some >> other >> smart way to achieve what I want (and by smart, I mean a way that isn't >> time- >> consuming and unusually error-prone)? I've already tried Googling, to no >> avail; I got, mostly, instructions about how to display surfaces in >> general. >> >> I should mention that I'm using a recent version of MacPyMol, on Mac OS X >> 10.6.7. >> >> Any tips are welcome. Thanks! >> >> Best regards, >> Ben >> -- >> For greater security, I support S/MIME encryption. >> >> >> >> ------------------------------------------------------------------------------ >> What Every C/C++ and Fortran developer Should Know! >> Read this article and learn how Intel has extended the reach of its >> next-generation tools to help Windows* and Linux* C/C++ and Fortran >> developers boost performance applications - including clusters. >> http://p.sf.net/sfu/intel-dev2devmay >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
