import cPickle, base64 try: from SimpleSession.versions.v52 import beginRestore,\ registerAfterModelsCB, reportRestoreError, checkVersion except ImportError: from chimera import UserError raise UserError('Cannot open session that was saved in a' ' newer version of Chimera; update your version') checkVersion([1, 6, 34357]) import chimera from chimera import replyobj replyobj.status('Restoring session...', \ blankAfter=0) replyobj.status('Beginning session restore...', \ blankAfter=0, secondary=True) beginRestore() def restoreCoreModels(): from SimpleSession.versions.v52 import init, restoreViewer, \ restoreMolecules, restoreColors, restoreSurfaces, \ restoreVRML, restorePseudoBondGroups, restoreModelAssociations molInfo = cPickle.loads(base64.b64decode('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')) resInfo = cPickle.loads(base64.b64decode('gAJ9cQEoVQZpbnNlcnRxAksATn2HVQtmaWxsRGlzcGxheXEDSwBOfYdVBG5hbWVxBEsATn2HVQVjaGFpbnEFSwBOfYdVDnJpYmJvbkRyYXdNb2RlcQZLAE59h1UCc3NxB0sATn2HVQhtb2xlY3VsZXEISwBOfYdVC3JpYmJvbkNvbG9ycQlLAE59h1UFbGFiZWxxCksATn2HVQpsYWJlbENvbG9ycQtLAE59h1UIZmlsbE1vZGVxDEsATn2HVQVpc0hldHENSwBOfYdVC2xhYmVsT2Zmc2V0cQ5LAE59h1UIcG9zaXRpb25xD11VDXJpYmJvbkRpc3BsYXlxEEsATn2HVQhvcHRpb25hbHERfVUEc3NJZHESSwBOfYd1Lg==')) atomInfo = cPickle.loads(base64.b64decode('gAJ9cQEoVQdyZXNpZHVlcQJLAE59h1UIdmR3Q29sb3JxA0sATn2HVQRuYW1lcQRLAE59h1UDdmR3cQVLAE59h1UOc3VyZmFjZURpc3BsYXlxBksATn2HVQVjb2xvcnEHSwBOfYdVCWlkYXRtVHlwZXEISwBOfYdVBmFsdExvY3EJSwBOfYdVBWxhYmVscQpLAE59h1UOc3VyZmFjZU9wYWNpdHlxC0sATn2HVQdlbGVtZW50cQxLAE59h1UKbGFiZWxDb2xvcnENSwBOfYdVDHN1cmZhY2VDb2xvcnEOSwBOfYdVD3N1cmZhY2VDYXRlZ29yeXEPSwBOfYdVBnJhZGl1c3EQSwBOfYdVC2xhYmVsT2Zmc2V0cRFLAE59h1USbWluaW11bUxhYmVsUmFkaXVzcRJLAE59h1UIZHJhd01vZGVxE0sATn2HVQhvcHRpb25hbHEUfXEVVQxzZXJpYWxOdW1iZXJxFoiIXYdzVQdkaXNwbGF5cRdLAE59h3Uu')) bondInfo = cPickle.loads(base64.b64decode('gAJ9cQEoVQVhdG9tc3ECXVUFbGFiZWxxA0sATn2HVQZyYWRpdXNxBEsATn2HVQtsYWJlbE9mZnNldHEFSwBOfYdVCGRyYXdNb2RlcQZLAE59h1UIb3B0aW9uYWxxB31VB2Rpc3BsYXlxCEsATn2HdS4=')) crdInfo = cPickle.loads(base64.b64decode('gAJ9cQEu')) surfInfo = {'category': (0, None, {}), 'probeRadius': (0, None, {}), 'pointSize': (0, None, {}), 'name': [], 'density': (0, None, {}), 'colorMode': (0, None, {}), 'useLighting': (0, None, {}), 'transparencyBlendMode': (0, None, {}), 'molecule': [], 'smoothLines': (0, None, {}), 'lineWidth': (0, None, {}), 'allComponents': (0, None, {}), 'twoSidedLighting': (0, None, {}), 'oneTransparentLayer': (0, None, {}), 'drawMode': (0, None, {}), 'display': (0, None, {}), 'customColors': []} vrmlInfo = {'subid': (0, None, {}), 'display': (0, None, {}), 'id': (0, None, {}), 'vrmlString': [], 'name': (0, None, {})} colors = {'Ru': ((0.141176, 0.560784, 0.560784), 1, u'default'), 'Ni': ((0.313725, 0.815686, 0.313725), 1, u'default'), 'Re': ((0.14902, 0.490196, 0.670588), 1, u'default'), 'Rf': ((0.8, 0, 0.34902), 1, u'default'), 'Ra': ((0, 0.490196, 0), 1, u'default'), 'Rb': ((0.439216, 0.180392, 0.690196), 1, u'default'), 'Rn': ((0.258824, 0.509804, 0.588235), 1, u'default'), 'Rh': ((0.0392157, 0.490196, 0.54902), 1, u'default'), 'Be': ((0.760784, 1, 0), 1, u'default'), 'Ba': ((0, 0.788235, 0), 1, u'default'), 'Bh': ((0.878431, 0, 0.219608), 1, u'default'), 'Bi': ((0.619608, 0.309804, 0.709804), 1, u'default'), 'Bk': ((0.541176, 0.309804, 0.890196), 1, u'default'), 'Br': ((0.65098, 0.160784, 0.160784), 1, u'default'), '_openColor00': ((1, 1, 1), 1, u'default'), '_openColor01': ((1, 0, 1), 1, u'default'), '_openColor02': ((0, 1, 1), 1, u'default'), '_openColor03': ((1, 1, 0), 1, u'default'), '_openColor04': ((1, 0, 0), 1, u'default'), '_openColor05': ((0, 0, 1), 1, u'default'), '_openColor06': ((0.67, 1, 0), 1, u'default'), '_openColor07': ((0.67, 0, 1), 1, u'default'), '_openColor08': ((0.67, 1, 1), 1, u'default'), 'H': ((1, 1, 1), 1, u'default'), 'P': ((1, 0.501961, 0), 1, u'default'), 'Os': ((0.14902, 0.4, 0.588235), 1, u'default'), 'Ge': ((0.4, 0.560784, 0.560784), 1, u'default'), 'Gd': ((0.270588, 1, 0.780392), 1, u'default'), 'Ga': ((0.760784, 0.560784, 0.560784), 1, u'default'), 'Pr': ((0.85098, 1, 0.780392), 1, u'default'), '_openColor12': ((1, 1, 0.5), 1, u'default'), '_openColor11': ((1, 0.67, 1), 1, u'default'), '_openColor10': ((0, 0.67, 1), 1, u'default'), 'Pt': ((0.815686, 0.815686, 0.878431), 1, u'default'), 'Pu': ((0, 0.419608, 1), 1, u'default'), 'C': ((0.564706, 0.564706, 0.564706), 1, u'default'), 'Pb': ((0.341176, 0.34902, 0.380392), 1, u'default'), 'Pa': ((0, 0.631373, 1), 1, u'default'), 'Pd': ((0, 0.411765, 0.521569), 1, u'default'), 'Xe': ((0.258824, 0.619608, 0.690196), 1, u'default'), 'Po': ((0.670588, 0.360784, 0), 1, u'default'), 'Pm': ((0.639216, 1, 0.780392), 1, u'default'), 'Hs': ((0.901961, 0, 0.180392), 1, u'default'), 'Ho': ((0, 1, 0.611765), 1, u'default'), 'Hf': ((0.301961, 0.760784, 1), 1, u'default'), 'Hg': ((0.721569, 0.721569, 0.815686), 1, u'default'), 'He': ((0.85098, 1, 1), 1, u'default'), 'Md': ((0.701961, 0.0509804, 0.65098), 1, u'default'), 'Mg': ((0.541176, 1, 0), 1, u'default'), 'K': ((0.560784, 0.25098, 0.831373), 1, u'default'), 'Mn': ((0.611765, 0.478431, 0.780392), 1, u'default'), 'O': ((1, 0.0509804, 0.0509804), 1, u'default'), 'Mt': ((0.921569, 0, 0.14902), 1, u'default'), 'S': ((1, 1, 0.188235), 1, u'default'), 'W': ((0.129412, 0.580392, 0.839216), 1, u'default'), 'Zn': ((0.490196, 0.501961, 0.690196), 1, u'default'), 'Eu': ((0.380392, 1, 0.780392), 1, u'default'), 'Zr': ((0.580392, 0.878431, 0.878431), 1, u'default'), 'Er': ((0, 0.901961, 0.458824), 1, u'default'), '_openColor13': ((1, 0, 0.5), 1, u'default'), 'No': ((0.741176, 0.0509804, 0.529412), 1, u'default'), 'Na': ((0.670588, 0.360784, 0.94902), 1, u'default'), 'Nb': ((0.45098, 0.760784, 0.788235), 1, u'default'), 'Nd': ((0.780392, 1, 0.780392), 1, u'default'), 'Ne': ((0.701961, 0.890196, 0.960784), 1, u'default'), 'Np': ((0, 0.501961, 1), 1, u'default'), 'Fr': ((0.258824, 0, 0.4), 1, u'default'), '_openColor15': ((0.67, 0.67, 1), 1, u'default'), '_openColor14': ((0, 1, 0.5), 1, u'default'), 'Fe': ((0.878431, 0.4, 0.2), 1, u'default'), 'Fm': ((0.701961, 0.121569, 0.729412), 1, u'default'), 'B': ((1, 0.709804, 0.709804), 1, u'default'), 'F': ((0.564706, 0.878431, 0.313725), 1, u'default'), 'Sr': ((0, 1, 0), 1, u'default'), 'N': ((0.188235, 0.313725, 0.972549), 1, u'default'), 'Kr': ((0.360784, 0.721569, 0.819608), 1, u'default'), 'Si': ((0.941176, 0.784314, 0.627451), 1, u'default'), 'Sn': ((0.4, 0.501961, 0.501961), 1, u'default'), 'Sm': ((0.560784, 1, 0.780392), 1, u'default'), 'V': ((0.65098, 0.65098, 0.670588), 1, u'default'), 'Sc': ((0.901961, 0.901961, 0.901961), 1, u'default'), 'Sb': ((0.619608, 0.388235, 0.709804), 1, u'default'), 'Sg': ((0.85098, 0, 0.270588), 1, u'default'), 'Se': ((1, 0.631373, 0), 1, u'default'), 'Co': ((0.941176, 0.564706, 0.627451), 1, u'default'), 'Cm': ((0.470588, 0.360784, 0.890196), 1, u'default'), 'Cl': ((0.121569, 0.941176, 0.121569), 1, u'default'), 'Ca': ((0.239216, 1, 0), 1, u'default'), 'Cf': ((0.631373, 0.211765, 0.831373), 1, u'default'), 'Ce': ((1, 1, 0.780392), 1, u'default'), 'Cd': ((1, 0.85098, 0.560784), 1, u'default'), 'Tm': ((0, 0.831373, 0.321569), 1, u'default'), 'Cs': ((0.341176, 0.0901961, 0.560784), 1, u'default'), 'Cr': ((0.541176, 0.6, 0.780392), 1, u'default'), 'Cu': ((0.784314, 0.501961, 0.2), 1, u'default'), 'La': ((0.439216, 0.831373, 1), 1, u'default'), 'Li': ((0.8, 0.501961, 1), 1, u'default'), 'Tl': ((0.65098, 0.329412, 0.301961), 1, u'default'), 'Lu': ((0, 0.670588, 0.141176), 1, u'default'), 'Lr': ((0.780392, 0, 0.4), 1, u'default'), 'Th': ((0, 0.729412, 1), 1, u'default'), 'Ti': ((0.74902, 0.760784, 0.780392), 1, u'default'), 'Te': ((0.831373, 0.478431, 0), 1, u'default'), 'Tb': ((0.188235, 1, 0.780392), 1, u'default'), 'Tc': ((0.231373, 0.619608, 0.619608), 1, u'default'), 'Ta': ((0.301961, 0.65098, 1), 1, u'default'), 'Yb': ((0, 0.74902, 0.219608), 1, u'default'), 'Db': ((0.819608, 0, 0.309804), 1, u'default'), 'Dy': ((0.121569, 1, 0.780392), 1, u'default'), '_openColor09': ((1, 0.67, 0), 1, u'default'), 'At': ((0.458824, 0.309804, 0.270588), 1, u'default'), 'I': ((0.580392, 0, 0.580392), 1, u'default'), 'U': ((0, 0.560784, 1), 1, u'default'), 'Y': ((0.580392, 1, 1), 1, u'default'), 'Ac': ((0.439216, 0.670588, 0.980392), 1, u'default'), 'Ag': ((0.752941, 0.752941, 0.752941), 1, u'default'), 'Ir': ((0.0901961, 0.329412, 0.529412), 1, u'default'), 'Am': ((0.329412, 0.360784, 0.94902), 1, u'default'), 'Al': ((0.74902, 0.65098, 0.65098), 1, u'default'), 'As': ((0.741176, 0.501961, 0.890196), 1, u'default'), 'Ar': ((0.501961, 0.819608, 0.890196), 1, u'default'), 'Au': ((1, 0.819608, 0.137255), 1, u'default'), 'Es': ((0.701961, 0.121569, 0.831373), 1, u'default'), 'In': ((0.65098, 0.458824, 0.45098), 1, u'default'), 'Mo': ((0.329412, 0.709804, 0.709804), 1, u'default')} materials = {u'default': ((0.85, 0.85, 0.85), 30)} pbInfo = {'category': [u'distance monitor'], 'bondInfo': [{'color': (0, None, {}), 'atoms': [], 'label': (0, None, {}), 'halfbond': (0, None, {}), 'labelColor': (0, None, {}), 'drawMode': (0, None, {}), 'display': (0, None, {})}], 'lineType': (1, 2, {}), 'color': (1, 0, {}), 'optional': {'fixedLabels': (True, False, (1, False, {}))}, 'display': (1, True, {}), 'showStubBonds': (1, False, {}), 'lineWidth': (1, 1, {}), 'stickScale': (1, 1, {}), 'id': [-2]} modelAssociations = {} colorInfo = {0: (u'yellow', (1, 1, 0, 1)), 1: (u'green', (0, 1, 0, 1))} viewerInfo = {'cameraAttrs': {'center': (-0.278, -0.278, 142.116), 'fieldOfView': 18.9132, 'nearFar': (955.342, -671.109), 'ortho': False, 'eyeSeparation': 50.8, 'focal': -252.44}, 'viewerAttrs': {'silhouetteColor': None, 'clipping': False, 'showSilhouette': False, 'viewSize': 574.328, 'depthCueRange': (0.5, 1), 'silhouetteWidth': 1, 'depthCue': True, 'highlight': 0, 'scaleFactor': 0.965708}, 'viewerHL': 1, 'cameraMode': 'mono', 'detail': 1, 'viewerFog': None, 'viewerBG': None} replyobj.status("Initializing session restore...", blankAfter=0, secondary=True) init(colorInfo) replyobj.status("Restoring colors...", blankAfter=0, secondary=True) restoreColors(colors, materials) replyobj.status("Restoring molecules...", blankAfter=0, secondary=True) restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo) replyobj.status("Restoring surfaces...", blankAfter=0, secondary=True) restoreSurfaces(surfInfo) replyobj.status("Restoring VRML models...", blankAfter=0, secondary=True) restoreVRML(vrmlInfo) replyobj.status("Restoring pseudobond groups...", blankAfter=0, secondary=True) restorePseudoBondGroups(pbInfo) replyobj.status("Restoring model associations...", blankAfter=0, secondary=True) restoreModelAssociations(modelAssociations) replyobj.status("Restoring camera...", blankAfter=0, secondary=True) restoreViewer(viewerInfo) try: restoreCoreModels() except: reportRestoreError("Error restoring core models") replyobj.status("Restoring extension info...", blankAfter=0, secondary=True) def restore_surface_color_mapping(): try: surface_color_state = \ { 'class': 'Surface_Colorings_State', 'coloring_table': { ( 1, 0, ): ( { 'class': 'Radial_Color_State', 'colormap': { 'class': 'Color_Map_State', 'color_above_value_range': ( 1.0, 1.0, 0.0, 1.0, ), 'color_below_value_range': ( 1.0, 0.0, 0.0, 1.0, ), 'color_no_value': ( 0.5, 0.5, 0.5, 1, ), 'colors': [ ( 1.0, 0.0, 0.0, 1.0, ), ( 1.0, 1.0, 0.0, 1.0, ), ], 'data_values': [ 56.0, 57.0, ], 'version': 1, }, 'origin': ( 196.6075, 269.4268, 6.5152, ), 'version': 1, }, 0, ), }, 'geometry': None, 'is_visible': False, 'version': 2, } import SurfaceColor.session SurfaceColor.session.restore_surface_color_state(surface_color_state) except: reportRestoreError('Error restoring surface color mapping') registerAfterModelsCB(restore_surface_color_mapping) def restore_hide_dust(): hide_dust_state = \ { 'class': 'Hide_Dust_State', 'dust_table': { ( 1, 0, ): ( 'size', 119.0, ), }, 'version': 1, } try: import HideDust.session HideDust.session.restore_hide_dust_state(hide_dust_state) except: reportRestoreError('Error restoring hide dust') registerAfterModelsCB(restore_hide_dust) def restore_surface_zones(): surface_zone_state = \ { 'class': 'Surface_Zone_State', 'version': 2, 'zone_table': {}, } try: import SurfaceZone.session SurfaceZone.session.restore_surface_zone_state(surface_zone_state) except: reportRestoreError('Error restoring surface zones') registerAfterModelsCB(restore_surface_zones) def restore_volume_data(): volume_data_state = \ { 'class': 'Volume_Manager_State', 'data_and_regions_state': [ ( { 'available_subsamplings': {}, 'cell_angles': ( 90.0, 90.0, 90.0, ), 'class': 'Data_State', 'file_type': 'mrc', 'grid_id': '', 'name': 'siv-one-plane.mrc', 'path': 'siv-one-plane.mrc', 'rotation': ( ( 1, 0, 0, ), ( 0, 1, 0, ), ( 0, 0, 1, ), ), 'symmetries': ( ), 'version': 6, 'xyz_origin': None, 'xyz_step': None, }, [ { 'class': 'Volume_State', 'default_rgba': ( 1.0, 1.0, 1.0, 1.0, ), 'region': ( ( 0, 0, 0, ), ( 2047, 2047, 0, ), ( 1, 1, 1, ), ), 'region_list': { 'class': 'Region_List_State', 'current_index': 0, 'named_regions': [ ], 'region_list': [ ( ( 0, 0, 0, ), ( 2047, 2047, 0, ), ), ], 'version': 1, }, 'rendering_options': { 'bt_correction': 0, 'cap_faces': 1, 'class': 'Rendering_Options_State', 'color_mode': 'auto8', 'dim_transparency': 1, 'dim_transparent_voxels': 1, 'flip_normals': 0, 'limit_voxel_count': 1, 'line_thickness': 1.0, 'linear_interpolation': 1, 'maximum_intensity_projection': 0, 'mesh_lighting': 1, 'minimal_texture_memory': 0, 'one_transparent_layer': 1, 'outline_box_linewidth': 1.0, 'outline_box_rgb': ( 1.0, 1.0, 1.0, ), 'projection_mode': 'auto', 'show_outline_box': 0, 'smooth_lines': 0, 'smoothing_factor': 0.3, 'smoothing_iterations': 2, 'square_mesh': 1, 'subdivide_surface': 0, 'subdivision_levels': 1, 'surface_smoothing': 0, 'two_sided_lighting': 1, 'version': 1, 'voxel_limit': 4.0, }, 'representation': 'solid', 'session_volume_id': '\x0cqeHhUN~%#?Y(z5\x0cGspfqOOLD634In/%', 'solid_brightness_factor': 1.0, 'solid_colors': [ ( 1.0, 1.0, 1.0, 1.0, ), ( 1.0, 1.0, 1.0, 1.0, ), ( 1.0, 1.0, 1.0, 1.0, ), ], 'solid_levels': [ ( 91.0, 1.0, ), ( 67.68799999999989, 1.0, ), ( -34.54999999999991, 0.0, ), ], 'solid_model': { 'active': True, 'class': 'Model_State', 'clip_plane_normal': ( 0.0, 0.0, -1.0, ), 'clip_plane_origin': ( 0.0, 0.0, 0.0, ), 'clip_thickness': 5.0, 'display': True, 'id': 3, 'name': u'siv-one-plane.mrc solid', 'osl_identifier': u'#3', 'subid': 0, 'use_clip_plane': False, 'use_clip_thickness': False, 'version': 4, 'xform': { 'class': 'Xform_State', 'rotation_angle': 28.465972100688692, 'rotation_axis': ( -0.982394550494137, 0.058672681326016836, 0.17736533941398483, ), 'translation': ( 19.44926225065969, -51.49564537568882, 150.80904621705346, ), 'version': 1, }, }, 'surface_brightness_factor': 1.0, 'surface_colors': [ ( 0.7, 0.7, 1, 1, ), ], 'surface_levels': [ -0.009799999999998477, ], 'surface_model': { 'active': True, 'class': 'Model_State', 'clip_plane_normal': ( 0.0, 0.0, -1.0, ), 'clip_plane_origin': ( 0.0, 0.0, 0.0, ), 'clip_thickness': 5.0, 'display': False, 'id': 3, 'name': u'siv-one-plane.mrc', 'osl_identifier': u'#3', 'subid': 0, 'use_clip_plane': False, 'use_clip_thickness': False, 'version': 4, 'xform': { 'class': 'Xform_State', 'rotation_angle': 28.465972100688692, 'rotation_axis': ( -0.982394550494137, 0.058672681326016836, 0.17736533941398483, ), 'translation': ( 19.44926225065969, -51.49564537568882, 150.80904621705346, ), 'version': 1, }, }, 'transparency_depth': 0.5, 'transparency_factor': 0.0, 'version': 6, }, ], ), ( { 'available_subsamplings': {}, 'cell_angles': ( 90.0, 90.0, 90.0, ), 'class': 'Data_State', 'file_type': 'mrc', 'grid_id': '', 'name': 'siv-virion.mrc', 'path': 'siv-virion.mrc', 'rotation': ( ( 1, 0, 0, ), ( 0, 1, 0, ), ( 0, 0, 1, ), ), 'symmetries': ( ), 'version': 6, 'xyz_origin': None, 'xyz_step': None, }, [ { 'class': 'Volume_State', 'default_rgba': ( 0.7, 0.7, 0.7, 1, ), 'region': ( ( 0, 0, 0, ), ( 141, 136, 126, ), ( 1, 1, 1, ), ), 'region_list': { 'class': 'Region_List_State', 'current_index': 0, 'named_regions': [ ], 'region_list': [ ( ( 0, 0, 0, ), ( 141, 136, 126, ), ), ], 'version': 1, }, 'rendering_options': { 'bt_correction': 0, 'cap_faces': 1, 'class': 'Rendering_Options_State', 'color_mode': 'auto8', 'dim_transparency': 1, 'dim_transparent_voxels': 1, 'flip_normals': 0, 'limit_voxel_count': 1, 'line_thickness': 1.0, 'linear_interpolation': 1, 'maximum_intensity_projection': 0, 'mesh_lighting': 1, 'minimal_texture_memory': 0, 'one_transparent_layer': 1, 'outline_box_linewidth': 1.0, 'outline_box_rgb': ( 1.0, 1.0, 1.0, ), 'projection_mode': 'auto', 'show_outline_box': 0, 'smooth_lines': 1, 'smoothing_factor': 0.3, 'smoothing_iterations': 2, 'square_mesh': 1, 'subdivide_surface': 0, 'subdivision_levels': 1, 'surface_smoothing': 0, 'two_sided_lighting': 1, 'version': 1, 'voxel_limit': 15.1, }, 'representation': 'surface', 'session_volume_id': 453399176, 'solid_brightness_factor': 1.0, 'solid_colors': [ ( 1.0, 1.0, 1.0, 1, ), ( 1.0, 1.0, 1.0, 1, ), ( 1.0, 1.0, 1.0, 1, ), ], 'solid_levels': [ ( -30.998000000000005, 0, ), ( 56.977000000000004, 0.99, ), ( 127.0, 1, ), ], 'solid_model': None, 'surface_brightness_factor': 1.0, 'surface_colors': [ ( 0.7, 0.7, 0.7, 1, ), ], 'surface_levels': [ 17.195257929083347, ], 'surface_model': { 'active': True, 'class': 'Model_State', 'clip_plane_normal': ( 0.0, 0.0, 1.0, ), 'clip_plane_origin': ( 0.0, 0.0, 0.0, ), 'clip_thickness': 5.0, 'display': True, 'id': 1, 'name': u'siv-virion.mrc', 'osl_identifier': u'#1', 'subid': 0, 'use_clip_plane': False, 'use_clip_thickness': False, 'version': 4, 'xform': { 'class': 'Xform_State', 'rotation_angle': 28.465972100688692, 'rotation_axis': ( -0.982394550494137, 0.058672681326016836, 0.17736533941398483, ), 'translation': ( 19.44926225065969, -51.49564537568882, 150.80904621705346, ), 'version': 1, }, }, 'transparency_depth': 0.5, 'transparency_factor': 0.0, 'version': 6, }, ], ), ], 'version': 2, } from VolumeViewer import session session.restore_volume_data_state(volume_data_state) try: restore_volume_data() except: reportRestoreError('Error restoring volume data') def restore_volume_dialog(): volume_dialog_state = \ { 'adjust_camera': 0, 'auto_show_subregion': 0, 'box_padding': '0', 'class': 'Volume_Dialog_State', 'data_cache_size': '512', 'focus_volume': '\x0cqeHhUN~%#?Y(z5\x0cGspfqOOLD634In/%', 'geometry': '397x350+849+65', 'histogram_active_order': [ 1, 0, ], 'histogram_volumes': [ 453399176, '\x0cqeHhUN~%#?Y(z5\x0cGspfqOOLD634In/%', ], 'immediate_update': 1, 'initial_colors': ( ( 0.7, 0.7, 0.7, 1, ), ( 1, 1, 0.7, 1, ), ( 0.7, 1, 1, 1, ), ( 0.7, 0.7, 1, 1, ), ( 1, 0.7, 1, 1, ), ( 1, 0.7, 0.7, 1, ), ( 0.7, 1, 0.7, 1, ), ( 0.9, 0.75, 0.6, 1, ), ( 0.6, 0.75, 0.9, 1, ), ( 0.8, 0.8, 0.6, 1, ), ), 'is_visible': True, 'max_histograms': '3', 'representation': 'solid', 'selectable_subregions': 0, 'show_on_open': 1, 'show_plane': 1, 'shown_panels': [ 'Feature buttons', 'Threshold and Color', 'Display style', ], 'subregion_button': 'button 2', 'use_initial_colors': 1, 'version': 12, 'voxel_limit_for_open': '256', 'voxel_limit_for_plane': '256', 'zone_radius': 2.0, } from VolumeViewer import session session.restore_volume_dialog_state(volume_dialog_state) try: restore_volume_dialog() except: reportRestoreError('Error restoring volume dialog') def restoreLightController(): import Lighting Lighting._setFromParams({'brightness': 1.1450001726013008, 'material': [30.0, (0.85, 0.85, 0.85), 1.0], 'back': [(0.3574067443365933, 0.6604015517481455, -0.6604015517481456), (1.0, 1.0, 1.0), 0.0], 'mode': 'two-point', 'key': [(-0.3574067443365933, 0.6604015517481455, 0.6604015517481456), (1.0, 1.0, 1.0), 1.0], 'quality': 'glossy', 'contrast': 0.7418758519094082, 'fill': [(0.2505628070857316, 0.2505628070857316, 0.9351131265310294), (1.0, 1.0, 1.0), 0.0]}) try: restoreLightController() except: reportRestoreError("Error restoring lighting parameters") def restoreSession_RibbonStyleEditor(): import SimpleSession import RibbonStyleEditor userScalings = [('aa', [[0.25, 0.25], [1.7, 0.25], [1.5, 0.25], [0.25, 0.25, 3, 0.25], [1.7, 0.25]]), ('helen2', [[0.4, 0.4], [1.7, 0.4], [2, 0.4], [2, 0.4, 0.4, 0.4], [0.9, 0.25]]), ('maya', [[0.2, 0.2], [1.2, 0.2], [1.2, 0.2], [1.8, 0.2, 0.2, 0.2], [0.9, 0.2]]), ('encyclo_virol_2006_FAT', [[0.6, 0.6], [1.5, 0.6], [1.5, 0.6], [3, 0.25, 0.25, 0.25], [0.6, 0.6]]), ('testdefault', [[0.25, 0.25], [1.5, 0.25], [1.5, 0.25], [3, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('80percent', [[0.2, 0.2], [1.2, 0.2], [1.2, 0.2], [2.4, 0.2, 0.2, 0.2], [1.2, 0.2]]), ('slim', [[0.2, 0.2], [1.2, 0.2], [1.2, 0.2], [2.4, 0.2, 0.2, 0.2], [1.2, 0.2]]), ('skinny', [[0.25, 0.25], [0.75, 0.25], [0.75, 0.25], [1.5, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('Liz1', [[0.5, 0.5], [0.9, 0.25], [0.9, 0.25], [1.8, 0.25, 0.25, 0.25], [0.9, 0.25]]), ('SUPERFAT', [[0.7, 0.7], [1.6, 0.7], [1.6, 0.7], [3.1, 0.35, 0.35, 0.35], [0.7, 0.7]]), ('narrow nucleic - gary', [[0.2, 0.2], [0.9, 0.2], [0.95, 0.2], [1.8, 0.2, 0.2, 0.2], [0.35, 0.2]]), ('60%', [[0.15, 0.15], [0.9, 0.15], [0.9, 0.15], [1.8, 0.15, 0.15, 0.15], [0.9, 0.15]]), ('minus_20%', [[0.2, 0.2], [1.2, 0.2], [1.2, 0.2], [2.4, 0.2, 0.2, 0.2], [1.2, 0.2]]), ('60_percent', [[0.15, 0.15], [0.9, 0.15], [0.9, 0.15], [2.4, 0.15, 0.15, 0.15], [0.9, 0.15]]), ('20%', [[0.05, 0.05], [0.3, 0.05], [0.3, 0.05], [0.6, 0.05, 0.05, 0.05], [0.3, 0.05]]), ('no-helix', [[0.25, 0.25], [0.25, 0.25], [1.5, 0.25], [3, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('for3Dprint1round', [[0.8, 0.8], [1.5, 0.8], [1.5, 0.8], [2.4, 0.8, 0.8, 0.8], [1, 0.6]]), ('BS', [[0.3, 0.3], [1.5, 0.3], [1.5, 0.3], [3, 0.3, 0.25, 0.3], [1.5, 0.3]]), ('ssccmv_ribbon_scale', [[0.3, 0.3], [1.25, 0.5], [1.25, 0.5], [2.25, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('fatz', [[0.25, 0.25], [2.5, 0.25], [2.5, 0.25], [3, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('spaghetti', [[0.25, 0.25], [0.25, 0.25], [0.25, 0.25], [0.25, 0.25, 0.25, 0.25], [0.25, 0.25]]), ('for3Dprint1', [[0.5, 0.5], [0.9, 0.5], [0.9, 0.5], [1.8, 0.5, 0.5, 0.5], [0.9, 0.5]]), ('Margy_thin', [[0.25, 0.25], [0.4, 0.25], [0.4, 0.25], [1.5, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('40%', [[0.1, 0.1], [0.6, 0.1], [0.6, 0.1], [1.2, 0.1, 0.1, 0.1], [0.6, 0.1]]), ('thin2', [[0.25, 0.15], [0.4, 0.15], [0.4, 0.15], [1, 0.15, 0.25, 0.15], [1.5, 0.25]]), ('histon_1_s1', [[0.25, 0.25], [1.5, 0.25], [1.5, 0.25], [3, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('default', [[0.25, 0.25], [1.5, 0.25], [1.5, 0.25], [0.25, 0.25, 3, 0.25], [1.5, 0.25]]), ('narrow nucleic 2 -gary', [[0.2, 0.2], [0.9, 0.2], [0.95, 0.2], [1.8, 0.2, 0.2, 0.2], [0.35, 0.35]]), ('user default', [[0.25, 0.25], [1.5, 0.25], [1.5, 0.25], [0.25, 0.25, 3, 0.25], [1.5, 0.25]]), ('licorice', [[0.35, 0.35], [0.35, 0.35], [0.35, 0.35], [0.35, 0.35, 0.35, 0.35], [0.35, 0.35]]), ('slim2029', [[0.2, 0.2], [1.2, 0.2], [1.2, 0.2], [2.4, 0.2, 0.2, 0.2], [1.2, 0.2]]), ('FAT', [[0.6, 0.6], [1.5, 0.6], [1.5, 0.6], [3, 0.25, 0.25, 0.25], [0.7, 0.7]]), ('thinturn', [[0.1, 0.25], [1.5, 0.25], [1.5, 0.25], [3, 0.25, 0.25, 0.25], [1.5, 0.25]]), ('linguini', [[0.1, 0.1], [0.1, 0.1], [0.1, 0.1], [0.1, 0.1, 0.1, 0.1], [0.1, 0.1]]), ('Margy_medium', [[0.45, 0.25], [0.7, 0.25], [0.7, 0.25], [1.5, 0.25, 0.45, 0.25], [1.5, 0.25]]), ('encyclo_virol_2006_STD', [[0.4, 0.4], [1.5, 0.4], [1.5, 0.4], [3, 0.25, 0.25, 0.25], [0.4, 0.4]]), ('thin', [[0.15, 0.15], [0.75, 0.15], [0.75, 0.15], [1.75, 0.15, 0.15, 0.15], [1.5, 0.25]]), ('thin even', [[0.4, 0.4], [0.4, 0.4], [0.4, 0.4], [0.4, 0.4, 0.4, 0.4], [1.5, 0.25]]), ('slimrib', [[0.2, 0.2], [1, 0.2], [1, 0.2], [0.2, 0.2, 2, 0.2], [1, 0.2]]), ('barrel', [[0.75, 0.75], [2, 0.75], [2, 0.75], [2.6, 0.75, 0.75, 0.75], [0.9, 0.25]]), ('60percent', [[0.15, 0.15], [0.9, 0.15], [0.9, 0.15], [1.8, 0.15, 0.15, 0.15], [0.9, 0.15]]), ('plump', [[0.3, 0.3], [1.2, 0.3], [1.2, 0.3], [2, 0.3, 0.3, 0.3], [1.2, 0.3]])] userXSections = [('', ([(4, 4), (5, 5), (6, 5), (7, 4), (7, 3), (6, 2), (5, 2), (4, 3)], 1, 1, 1, 10)), ('diamond', ([(3, 3), (0, 5), (3, 7), (7, 7), (10, 5), (7, 3)], 0, 1, 1, 10)), ('large_octagon', ([(1, 3), (1, 5), (3, 7), (5, 7), (7, 5), (7, 3), (5, 1), (3, 1)], 1, 1, 1, 8)), ('octagon', ([(4, 4), (5, 5), (6, 5), (7, 4), (7, 3), (6, 2), (5, 2), (4, 3)], 1, 1, 1, 10)), ('thin_round_square', ([(4, 2), (5, 2), (6, 5), (4, 3), (4, 4), (4, 5), (6, 4), (5, 4), (5, 3), (6, 3)], True, True, True, 10)), ('ibeam', ([(10, 0), (8, 0), (8, 4), (2, 4), (2, 0), (0, 0), (0, 10), (2, 10), (2, 6), (8, 6), (8, 10), (10, 10)], 0, 1, 1, 10)), ('aitch', ([(0, 0), (0, 10), (3, 10), (3, 6), (7, 6), (7, 10), (10, 10), (10, 0), (7, 0), (7, 4), (3, 4), (3, 0), (0, 0)], 1, True, False, 10)), ('ocatagon', ([(4, 4), (5, 5), (6, 5), (7, 4), (7, 3), (6, 2), (5, 2), (4, 3)], 1, 1, 1, 10)), ('wave', ([(18, 18), (18, 19), (18, 31), (31, 31), (31, 18)], True, True, True, 50))] userResidueClasses = [('aa-nomain-ca-o', ('CA', 'O', False, False, {})), ('aa-camain-ca-n', ('CA', 'N', False, False, {'CA': 0.5})), ('aa-camain-ca-o', ('CA', 'O', False, False, {'CA': 0.5})), ('aa-camain-ca-c', ('CA', 'C', False, False, {'CA': 0.5})), ('pguide', ('P', "C1'", False, True, {"C5'": 0.5, 'P': 0.166667, "O3'": 1, 'O1P': 0.166667, 'O3P': 0.166667, "O5'": 0.333333, 'O3T': 1, 'O2P': 0.166667, 'O5T': 0})), ('aa-nomain-c-o', ('C', 'O', False, False, {})), ('pguiderot', ('P', "C1'", 1, True, {"C5'": 0.5, 'P': 0.166667, "O3'": 1, 'O1P': 0.166667, 'O3P': 0.166667, "O5'": 0.333333, 'O3T': 1, 'O2P': 0.166667, 'O5T': 0}))] residueData = [] flags = RibbonStyleEditor.NucleicDefault1 SimpleSession.registerAfterModelsCB(RibbonStyleEditor.restoreState, (userScalings, userXSections, userResidueClasses, residueData, flags)) try: restoreSession_RibbonStyleEditor() except: reportRestoreError("Error restoring RibbonStyleEditor state") geomData = {'AxisManager': {}, 'CentroidManager': {}, 'PlaneManager': {}} try: from StructMeasure.Geometry import geomManager geomManager._restoreSession(geomData) except: reportRestoreError("Error restoring geometry objects in session") def restoreMidasText(): from Midas import midas_text midas_text.aliases = {} midas_text.userSurfCategories = {} try: restoreMidasText() except: reportRestoreError('Error restoring Midas text state') def restoreMidasBase(): import chimera from SimpleSession import modelMap, modelOffset def deformatPosition(pos): xfDict = {} for molId, xfData in pos[5].items(): mid, subid = molId trData, rotData = xfData xf = chimera.Xform.translation(*trData) xf.rotate(*rotData) xfDict[(mid+modelOffset, subid)] = xf try: from chimera.misc import KludgeWeakWrappyDict clipDict = KludgeWeakWrappyDict("Model") except ImportError: from weakref import WeakKeyDictionary clipDict = WeakKeyDictionary() for clipID, clipInfo in pos[6].items(): mid, subid, className = clipID models = [m for m in modelMap.get((mid, subid), []) if m.__class__.__name__ == className] if not models: continue useClip, ox, oy, oz, nx, ny, nz, useThick, thickness = clipInfo if useClip: origin = chimera.Point(ox, oy, oz) normal = chimera.Vector(nx, ny, nz) plane = chimera.Plane(origin, normal) else: plane = chimera.Plane() for m in models: clipDict[m] = (useClip, plane, useThick, thickness) return pos[:5] + (xfDict, clipDict) + pos[7:] formattedPositions = {'session-start': (0.965708, 574.328, (-0.278, -0.278, 142.116), (955.342, -671.109), -252.44, {(3, 0): ((19.44926225065969, -51.49564537568882, 150.80904621705346), (-0.982394550494137, 0.058672681326016836, 0.17736533941398483, 28.465972100688692)), (1, 0): ((19.44926225065969, -51.49564537568882, 150.80904621705346), (-0.982394550494137, 0.058672681326016836, 0.17736533941398483, 28.465972100688692))}, {(1, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, False, 5.0), (3, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, False, 5.0), (3, 0, 'Volume_Model'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, False, 5.0)}, 4, (19.12882247276957, -56.46050655102681, 142.11639924746055), False, 18.9132)} positions = {} for name, fpos in formattedPositions.items(): positions[name] = deformatPosition(fpos) import Midas if modelOffset == 0: Midas.positions.clear() Midas.positions.update(positions) def delayedMidasBase(): try: restoreMidasBase() except: reportRestoreError('Error restoring Midas base state') import SimpleSession SimpleSession.registerAfterModelsCB(delayedMidasBase) try: import StructMeasure from StructMeasure.DistMonitor import restoreDistances registerAfterModelsCB(restoreDistances, 1) except: reportRestoreError("Error restoring distances in session") def restoreRemainder(): from SimpleSession.versions.v52 import restoreWindowSize, \ restoreOpenStates, restoreSelections, restoreFontInfo, \ restoreOpenModelsAttrs, restoreModelClip curSelIds = [] savedSels = [] openModelsAttrs = { 'cofrMethod': 4 } windowSize = (732, 633) xformMap = {} fontInfo = {'face': ('Sans Serif', 'Normal', 16)} clipPlaneInfo = {} replyobj.status("Restoring window...", blankAfter=0, secondary=True) restoreWindowSize(windowSize) replyobj.status("Restoring open states...", blankAfter=0, secondary=True) restoreOpenStates(xformMap) replyobj.status("Restoring font info...", blankAfter=0, secondary=True) restoreFontInfo(fontInfo) replyobj.status("Restoring selections...", blankAfter=0, secondary=True) restoreSelections(curSelIds, savedSels) replyobj.status("Restoring openModel attributes...", blankAfter=0, secondary=True) restoreOpenModelsAttrs(openModelsAttrs) replyobj.status("Restoring model clipping...", blankAfter=0, secondary=True) restoreModelClip(clipPlaneInfo) replyobj.status("Restoring remaining extension info...", blankAfter=0, secondary=True) try: restoreRemainder() except: reportRestoreError("Error restoring post-model state") from SimpleSession.versions.v52 import makeAfterModelsCBs makeAfterModelsCBs() from SimpleSession.versions.v52 import endRestore replyobj.status('Finishing restore...', blankAfter=0, secondary=True) endRestore() replyobj.status('', secondary=True) replyobj.status('Restore finished.')