Hi Timo, That is best approached with CGO objects. You can find some examples in \PyMOL\PyMOL\modules\pymol\cgo.py
Here is a bit of a write-up I attempted a while ago. BTW transparency of CGO objects can be controlled via the "setting cgo_transparency" HTH Carsten ---------------------------------------------------------------------------------------------------- Lines ===== The LINES command draws a lines between a set of coordinates defined by the VERTEX command. The colour of the lines can be changed at any time even between vertices, so that the start and end line color can be different. The color of the line will be interpolated between the start and end color. The thickness of the line is set by LINEWIDTH. However there is a bug in the implementation. The GL renderer accepts the LINEWIDTH statement only before a BEGIN statement. The internal renderer honors the change of the linewidth before every VERTEX pair. Note: Tapered lines are not supported by either implementation. LINEWIDTH and COLOR are optional commands. LINEWIDTH, w, BEGIN, LINES, COLOR, r, g, b, VERTEX, x1,y1,z1, VERTEX, x2,y2,z2, END Line Strips ============ The LINE_STRIP command draws a continuous line between sets of coordinates defined by the VERTEX command. The main difference to the LINES command is that the endpoint of the first line is automatically the start of the next line, but the first and last point are NOT connected, see LINE_LOOP instead. The colour of the lines can be changed at any time even between vertices, so that the start and end line color can be different. The color of the line will be interpolated between the start and end color. The thickness of the line is set by LINEWIDTH. However there is a bug in the implementation. The GL renderer accepts the LINEWIDTH statement only before a BEGIN statement. The internal renderer honors the change of the linewidth before every VERTEX pair. Note: Tapered lines are not supported by either implementation. LINEWIDTH and COLOR are optional commands. LINEWIDTH, w, BEGIN, LINE_STRIP, COLOR, r, g, b, VERTEX, x1,y1,z1, VERTEX, x2,y2,z2, ... VERTEX, xn,yn,zn END -----Original Message----- From: Timo Stein [mailto:m...@timo-stein.com] Sent: Friday, July 12, 2013 4:39 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Creating coloured and transparent polyhedra Hello PyMOL users, I'm using PyMOL to create fancy images of Metal-Organic Framework structural units. They feature metal ions of different coordination spheres. The structural features of these units can be clarified by showing the corresponding coordination polyhedron (for example of the metal ions colour) with the coordinating atoms sitting on the polyhedron's corners. The polyhedron should be quite transparent. How can you draw such polyhedrons with PyMOL? The Google image search for MOF-5 gives some examples of structures showing these coordination polyhedra. Thank you very much! Timo Stein ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ 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 ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ 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
