> Dear Developers, > > I have just downloaded and installed jmol. It seems very nice and > fast. My favorite area is the transmembrane proteins, and I would like to > show these proteins in membrane. Previously I use pymol, where extra > graphics can be generated using CGO, therefore I was able to present > transmembrane proteins with two additional planes (see pictures on PDB_TM > homepage, http://pdbtm.enzim.hu). It is possible to draw membrane planes > similarly by using jmol?
Yes. Jmol has support for pmesh (polygon mesh) files that allow one to build meshes of points in 3D space that define surfaces. > If yes, how can I do that. One can easily construct a plane plane by defining one polygon that defines the 4 corners of the plane. ---------- 4 # number of points 1.0 1.0 0.0 # point coordinates 1.0 -1.0 0.0 -1.0 -1.0 0.0 -1.0 1.0 0.0 1 # number of polygons 5 # number of points in this polygon WITH start point duplicated 0 1 2 3 0 # start point is duplicated ---------- load "your/molecule" pmesh plane1 "path/to/plane1.pmesh" color pmesh translucent orange pmesh plane2 "path/to/plane2.pmesh" color pmesh purple ... pmesh plane1 color pmesh green pmesh plane2 color pmesh translucent cornflowerblue Miguel ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
