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From: Yarrow M. <ama...@uc...> - 2013-03-04 19:38:08
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Thank you for your help Thomas, Using your settings I get a lot of "partial surfaces" Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow > Hi Yarrow, > should be as simple as: > PyMOL> hide surface > PyMOL> show surface, (organic around 8.0) > PyMOL> set transparency, 0.3 > PyMOL> set two_sided_lighting > See also: > http://pymolwiki.org/index.php/Selection_Algebra > Hope that helps. > Cheers, > Thomas > Yarrow Madrona wrote, On 03/03/13 18:34: >> Hello, >> Does anyone know how to visualize a surface within a given radius from a >> ligand binding site? In chimera you can limit the display surface within >> 0-X angstrom of a ligand. This allows you to see the surface surrounding >> the ligand without the rest of the protein. >> I guess you could create a new selection of residues around a ligand and >> show this surface but I wondered if there are any other ways of doing this. > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 |
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From: Sampson, J. <Jar...@ny...> - 2013-03-04 20:40:48
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Hi Yarrow - If you add "br. " to the show surface command, you will get more continuous surfaces, as the selection will be made by residue instead of by atom. show surface, br. protein within 0.5 of pocket_selection If you don't want to show the surface from a particular residue (e.g. if it's masking something else you want to show), you can hide surface for a selection. hide surface, resi 225+347 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 4, 2013, at 2:37 PM, Yarrow Madrona <ama...@UC...<mailto:ama...@UC...>> wrote: Thank you for your help Thomas, Using your settings I get a lot of "partial surfaces" Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow Hi Yarrow, should be as simple as: PyMOL> hide surface PyMOL> show surface, (organic around 8.0) PyMOL> set transparency, 0.3 PyMOL> set two_sided_lighting See also: http://pymolwiki.org/index.php/Selection_Algebra Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/03/13 18:34: Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 <screenshot.png>------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
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From: Jason V. <jas...@sc...> - 2013-03-05 05:00:18
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Greetings, Please also investigate the following settings: # needs a real atom selection surface_carve_selection # distance from the above selection to cull surfaces surface_carve_cutoff I looked at your data and there is a small problem. You have a few points where one atom is mapped to multiple surface points. Thus, when you show it as surface two pocket fragments show up. When you hide it they both hide. Also of interest is PyMOL's ability to render pockets and cavities on its own (Settings > Surface > Cavities & Pockets). Cheers, -- Jason On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared <Jar...@ny...>wrote: > Hi Yarrow - > > If you add "br. " to the show surface command, you will get more > continuous surfaces, as the selection will be made by residue instead of by > atom. > > show surface, br. protein within 0.5 of pocket_selection > > > If you don't want to show the surface from a particular residue (e.g. if > it's masking something else you want to show), you can hide surface for a > selection. > > hide surface, resi 225+347 > > > Cheers, > Jared > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > Old Public Health Building, Room 610 > 341 East 25th Street > New York, NY 10016 > 212-263-7898 > http://kong.med.nyu.edu/ > > > > > On Mar 4, 2013, at 2:37 PM, Yarrow Madrona <ama...@UC...> wrote: > > Thank you for your help Thomas, > > Using your settings I get a lot of "partial surfaces" > > Showing the surface around the Pocket selection like this: > > show surface, protein within 0.5 of pocket_selection > > worked well but I still see a piece of surface that I really don't want to > show up. I guess I can take it out in photoshop but that just seems wrong. > I have attached it. > > -Yarrow > > > > Hi Yarrow, > should be as simple as: > PyMOL> hide surface > PyMOL> show surface, (organic around 8.0) > PyMOL> set transparency, 0.3 > PyMOL> set two_sided_lighting > See also: > http://pymolwiki.org/index.php/Selection_Algebra > Hope that helps. > Cheers, > Thomas > Yarrow Madrona wrote, On 03/03/13 18:34: > > Hello, > Does anyone know how to visualize a surface within a given radius from > > a > > ligand binding site? In chimera you can limit the display surface > > within > > 0-X angstrom of a ligand. This allows you to see the surface > > surrounding > > the ligand without the rest of the protein. > I guess you could create a new selection of residues around a ligand > > and > > show this surface but I wondered if there are any other ways of doing > > this. > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > ------------------------------------------------------------------------------ > > Everyone hates slow websites. So do we. > > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697 > > <screenshot.png> > ------------------------------------------------------------------------------ > > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > > http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
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From: Yarrow M. <ama...@uc...> - 2013-03-05 17:40:34
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Thank you both for your kind help. I will follow this up today and let you know how it goes. -Yarrow > Greetings, > > Please also investigate the following settings: > > # needs a real atom selection > surface_carve_selection > > # distance from the above selection to cull surfaces > surface_carve_cutoff > > I looked at your data and there is a small problem. You have a few points > where one atom is mapped to multiple surface points. Thus, when you show > it > as surface two pocket fragments show up. When you hide it they both hide. > > Also of interest is PyMOL's ability to render pockets and cavities on its > own (Settings > Surface > Cavities & Pockets). > > Cheers, > > -- Jason > > > On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared > <Jar...@ny...>wrote: > >> Hi Yarrow - >> >> If you add "br. " to the show surface command, you will get more >> continuous surfaces, as the selection will be made by residue instead of >> by >> atom. >> >> show surface, br. protein within 0.5 of pocket_selection >> >> >> If you don't want to show the surface from a particular residue (e.g. >> if >> it's masking something else you want to show), you can hide surface for >> a >> selection. >> >> hide surface, resi 225+347 >> >> >> Cheers, >> Jared >> >> -- >> Jared Sampson >> Xiangpeng Kong Lab >> NYU Langone Medical Center >> Old Public Health Building, Room 610 >> 341 East 25th Street >> New York, NY 10016 >> 212-263-7898 >> http://kong.med.nyu.edu/ >> >> >> >> >> On Mar 4, 2013, at 2:37 PM, Yarrow Madrona <ama...@UC...> wrote: >> >> Thank you for your help Thomas, >> >> Using your settings I get a lot of "partial surfaces" >> >> Showing the surface around the Pocket selection like this: >> >> show surface, protein within 0.5 of pocket_selection >> >> worked well but I still see a piece of surface that I really don't want >> to >> show up. I guess I can take it out in photoshop but that just seems >> wrong. >> I have attached it. >> >> -Yarrow >> >> >> >> Hi Yarrow, >> should be as simple as: >> PyMOL> hide surface >> PyMOL> show surface, (organic around 8.0) >> PyMOL> set transparency, 0.3 >> PyMOL> set two_sided_lighting >> See also: >> http://pymolwiki.org/index.php/Selection_Algebra >> Hope that helps. >> Cheers, >> Thomas >> Yarrow Madrona wrote, On 03/03/13 18:34: >> >> Hello, >> Does anyone know how to visualize a surface within a given radius from >> >> a >> >> ligand binding site? In chimera you can limit the display surface >> >> within >> >> 0-X angstrom of a ligand. This allows you to see the surface >> >> surrounding >> >> the ligand without the rest of the protein. >> I guess you could create a new selection of residues around a ligand >> >> and >> >> show this surface but I wondered if there are any other ways of doing >> >> this. >> >> -- >> Thomas Holder >> PyMOL Developer >> Schrödinger Contractor >> >> ------------------------------------------------------------------------------ >> >> Everyone hates slow websites. So do we. >> >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_feb >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> Archives: http://www.mail-archive.com/pym...@li... >> >> >> -- >> Yarrow Madrona >> >> Graduate Student >> Molecular Biology and Biochemistry Dept. >> University of California, Irvine >> Natural Sciences I, Rm 2403 >> Irvine, CA 92697 >> >> <screenshot.png> >> ------------------------------------------------------------------------------ >> >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> >> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> >> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_feb >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 |
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