PyMOL's default behavior is dependent upon map file type: CCP4 and O/BRIX/DSN6 maps are automatically normalized upon reading (disable via normalize_* settings), other maps types are not. Some visualization tools automatically normalize maps upon reading, others do not. Generally speaking there is some ambiguity with visualization tools as to how map data is to treated: Some map file formats are normalized by convention (in the file data itself) and others do not.In thisĬase, symmetry information (lattice constants, space group) of the model specified in the selectionĪrgument if available, or (new in 1.7) from the map object. When map_auto_expand_sym is ON, you can create mesh beyond the precalculated volume. Isomesh normal, fake_map, 1.0, center MAP OUTSIDE THE CALCULATED AREA You can create mesh around the center of the view by specifying "center" as the selection argument.
If the mesh object already exists, then the new mesh will be appended onto the object as a new state (unless you indicate a state). The arguments selection, buffer and carve can limit the mesh display to a selected area, and/or extend the area by symmetry operators if the selection is located outside the map bounding box itself. Fetch 6 sps fetch 6 sps, type = 2 fofc # mesh for entire map object isomesh mesh_all, 6 sps_2fofc # mesh within bounding box of ligand, enlarged by 2 Angstrom isomesh mesh_ligand, 6 sps_2fofc, selection = ( resn LR5 ), buffer = 2 # mesh only within 2 Angstrom radius of any ligand atom isomesh mesh_ligand_carved, 6 sps_2fofc, selection = ( resn LR5 ), carve = 2 set_view (\Ġ.001600198, - 0.993020296, 0.117938228 ,\
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