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The surface representation of a protein, in PyMol, shows the "Connolly" surface or the surface that would be traced out by the surfaces of waters in contact with the protein at all possible positions. Surface Representation ExampleContents 1 Enabling 2 Settings 2.1 Examples 2.1.1 Transparency 2.1.2 Quality 2.1.3 Probe Radius 3 Tips 3.1 Exporting Surface/Mesh Coordinates to File 3.1.1 Older PyMOL Versions 3.1.2 Newer PyMOL Versions 3.2 Representation-independent Color Control 3.3 Displaying a protein as surface with a ligand as sticks 3.4 Calculating a partial surface 3.5 Displaying surface inside a molecule 3.6 Creating a Closed Surface 3.7 Smooth surface quick (blob) 3.8 Smooth surface accurate (blob) 3.9 Huge Surfaces 4 Performance Enabling To enable the surface representation do show surface, SELfor any proper selection SEL. Settings cavity_cull surface_best surface_negative_color surface_carve_cutoff surface_negative_visible surface_carve_normal_cutoff surface_normal surface_carve_selection surface_optimize_subsets surface_carve_state surface_poor surface_circumscribe surface_proximity surface_clear_cutoff surface_quality surface_clear_selection surface_ramp_above_mode surface_clear_state surface_solvent surface_color surface_trim_cutoff surface_debug surface_trim_factor surface_miserable surface_type surface_mode Examples TransparencyTo adjust the transparency of surfaces try: set transparency, 0.5Where 1.0 will be an invisible and 0.0 a completely solid surface. QualityTo smooth your surface representation try: set surface_quality, 1or higher if you wish, though it will take longer and might look odd. Probe RadiusTo change the probe radius other than default 1.4 脜, you need to change the solvent radius, say, 1.6 脜: set solvent_radius, 1.6If the surface does not change correspondingly, use: rebuild Tips Exporting Surface/Mesh Coordinates to FilePyMOL can export its coordinates as WRL wireframe model files for VRML input. Older PyMOL Versions # export the coordinates to povray open("surface.inc","w").write(cmd.get_povray()[1]) Newer PyMOL Versions # export the coordinates to .wrl file save myscene.wrlor # export the coordinates to .obj file. Only surface representation can be saved as .obj. # NOTE: the coordinates are saved in camera coordinate system. save myscene.obj Representation-independent Color ControlTo color the surface representation a different color than the underlying cartoon or ligand representations, simply duplicate the object, show only the surface in the duplicate, and show only the cartoon and/or ligands in the original object. Or use the surface_color setting that is available. Representation-independent Color Control Example Displaying a protein as surface with a ligand as sticks An easy way to do this is to create separate objects for each type of display. 1 Load your protein 2 Select the ligand 3 Create a separate object for the ligand 4 Remove ligand atoms from the protein 5 Display both objects separately Example: load prot.ent,protein select ligand,resn FAD create lig_sticks,ligand remove ligand show sticks,lig_sticks show surface,proteinEven easier is to: 1 Load the protein 2 S (Show) > organic > stick 3 S (Show) > surface Calculating a partial surfaceThere is, until now, an undocumented way to calculate a surface for only a part of an object without creating a new one: flag ignore, not A/49-63/, set delete indicate show surfaceIf the surface was already computed, then you'll also need to issue the command: rebuildSee Get_Area for more information on surface area calculations. Displaying surface inside a moleculeAs far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is: set ambient=0 set direct=0.7 set reflect=0.0 set backface_cull=0Which gives no shadows and only a few artifacts. As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray". util.ray_shadows("heavy") set two_sided_lighting=1 set backface_cull=0 Creating a Closed SurfaceExample OPEN Surface Example CLOSED Surface To create what I'll call a closed surface (see images), you need to first make your atom selections, then create a new object for that selection then show the surface for that object. Here's an example. sel A, id 1-100 create B, A show surface, B Smooth surface quick (blob)To get a quick blob type surface (not as accurate): set solvent_radius, 4 alter all, vdw=4 sort set surface_quality, 1 Smooth surface accurate (blob)To get an accurate blob type surface: set surface_quality, 1 alter all, b=50 alter all, q=1 set gaussian_resolution,5 map_new mapA, gaussian, 1, sele or pdb, 6 isosurface surfA, mapANotes: Set gaussian resolution is variable with a larger number causing a more smooth surface (4 is medium and 8 is very smooth). The temperature factor field (b) has at least as much impact as the resolution setting, so increasing b factors is the more computationally efficient way of increasing the blur effect. If you are displaying more then one surface in a .pse file you must create a new map for each one (if you have three you will create mapA for the first, mapB for the second and mapC for the third), then you apply an isosurface to each map (isosurface surfA, mapA - isosurface surfB, mapB - isosurface surfC, mapC). Huge SurfacesIf your protein or complex is too large to render (ray runs out of RAM, for example) then check out the tip for huge surfaces. PerformanceTo optimize performance and responsiveness, PyMOL tends to defer compute-intensive tasks until their results are actually needed. Thus, cmd.show("surface")doesn't actually show a surface, it only sets the surface visibility flag on the atoms present (for future reference). An actual surface won't be computed until PyMOL is asked to refresh or render the display. When running a script, you can force an update by calling: cmd.refresh()after cmd.show. |
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