[PyMOL] How to construct a view showing only a single contiguous cavity
Hi all, Thanks to Michael and Jason for their suggestions. I apologise for starting a new thread; I had inadvertently deleted the email conversation. I looked into hollow, but since the binding pocket is large and very irregularly shaped, it seemed as though it would be tricky to include the whole binding pocket without also including areas I didn't want, such as nearby cavities and pockets. Also, the surface carving was slow because my system is very large (the protein is roughly 35,000 atoms). So in the end I devised some aliases and constructed the binding pocket's surface piecemeal. Painstaking, but it got the job done :-) Thanks again, Ben -- For greater security, I support S/MIME encryption. smime.p7s Description: S/MIME cryptographic signature -- vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1___ 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
Re: [PyMOL] How to construct a view showing only a single contiguous cavity
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)
[PyMOL] How to construct a view showing only a single contiguous cavity
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. smime.p7s Description: S/MIME cryptographic signature -- 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
Re: [PyMOL] How to construct a view showing only a single contiguous cavity
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
