Comments on: Display Electron Density Map from the EDS in Pymol http://www.P212121.com/2009/06/18/display-electron-density-map-from-the-electron-density-server-in-pymol/ Protein Crystallography there is an Easier Way Wed, 10 Mar 2010 23:05:35 -0500 http://wordpress.org/?v=2.8.5 hourly 1 By: Matt k http://www.P212121.com/2009/06/18/display-electron-density-map-from-the-electron-density-server-in-pymol/comment-page-1/#comment-1045 Matt k Wed, 01 Jul 2009 02:53:01 +0000 http://www.P212121.com/?p=2358#comment-1045 I believe mesh as portrayed is showing a wireframe surface of the pdb file, not contouring the electron density map. The fact that sticks, lines spheres etc are options in the drop down menu is indicative of the pdb file (with a map the options should be mesh/surface/slice). The mesh inherits atom colours from the atoms, hence its rather colourful appearance. To make a density map using the drop down menu you can use the mesh option associated with the map, but using the density wizard is much more practical as it allows you to control the map size so you can ray trace without crashing. Nice to have someone blogging about crystallography, btw. I'm amazed that you find the time. I believe mesh as portrayed is showing a wireframe surface of the pdb file, not contouring the electron density map. The fact that sticks, lines spheres etc are options in the drop down menu is indicative of the pdb file (with a map the options should be mesh/surface/slice). The mesh inherits atom colours from the atoms, hence its rather colourful appearance. To make a density map using the drop down menu you can use the mesh option associated with the map, but using the density wizard is much more practical as it allows you to control the map size so you can ray trace without crashing.

Nice to have someone blogging about crystallography, btw. I’m amazed that you find the time.

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