[PyMOL] Making 3D-pdf's and keeping selections/colors
Hi Pymolers. I tried today the directions on http://pymolwiki.org/index.php/3d_pdf It works fine, and I have pdf with my pymol figure. But the colors and selections are not as when I save as .idtf. I just get a plain blue cartoon representation. Does anyone know where I should change something? - When saving as .idtf. - When converting to .u3d - Or when using movie15 package? Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 -- 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 (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
[PyMOL] [PyMol] How to visualize surface within a given radius
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. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- 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 (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] [PyMol] How to visualize surface within a given radius
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 (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
