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- Freshtime:2021-09-16
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Description
pymol 2.5
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
Exclusive Incentive PyMOL Features
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Multi-level undo/redo for all PyMOL actions
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MAE import: more ribbon styles and label improvements
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MAE import dialog: discrete states support
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Builder: Nucleotides from the PDB can now be extended
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APBS plugin: PDB2PQR 3 compatibility
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STL export: average normals when exporting
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`sphere_mode` s 10/11 scaled
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Builder: “Remove Residue” button added
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Load collada as CGO
File Import/Export
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DX binary map import support (*dxbin)
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PDB/MMTF export: symmetry information now added
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Improved FASTA import
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Support for map.gz and mrc.gz extensions
Builder & Panels
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Builder: Improved fuse command (disallows hypervalent bonds, substitute monovalent atoms instead of attaching to them)
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Panel: Customizable Keyboard Shortcut Menu
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Panel: Properties inspector now supports unsetting settings with “Delete” key
Graphics & Visualization
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Ray interior colors now match primitives with `set ray_interior_color, atomic` 120
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Isomesh transparency support
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`sphere_mode` 5 removed (9 as replacement)
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Curved cartoon cylindrical helices `cartoon_cylindrical_helices=1` (previous =2) . #131
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Isosurface generation via marching cubes with setting `isosurface_algorithm, (0, 1)` (0 requires VTKm)
PBC Handling
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Periodic boundary conditions supported in rebond, smooth, and intra_fit
API CHANGES
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Python 2 support removed
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pbc argument added to rebond, smooth, and intra_fit
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png(None) returns bytes
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scene_order() allows list for `names`
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pbc_wrap() and pbc_unwrap added
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matrix_reset() supports `state=0` for all states
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editing_ring() added
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unset now restores the default value for global settings
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load_traj now uses state=1 by default
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get_area command and dots representation: Exclude “flag ignore” atoms