https://wiki.pymol.org/api.php?action=feedcontributions&feedformat=atom&user=Saper 2026-05-25T08:31:55Z User contributions MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Talk:DrawBoundingBox&diff=13099 2015-08-25T17:25:50Z

<p>Saper: </p> <hr /> <div>Fixed two errors in the script:<br /> <br /> #&quot;if&quot; was indented incorrectly<br /> #&quot;sel&quot; was changed to &quot;selection&quot; for get_extent<br /> <br /> 8/25/2015 - This routine, does not find the minimum box. It does not find an orientation which minimizes the extents. Does anyone know how to do this? I'll have to think about it.</div>

Saper https://wiki.pymol.org/index.php?title=Settings&diff=10153 2010-06-29T19:13:32Z

<p>Saper: Added surface_cavity settings, but no pages for 2 of them.</p> <hr /> <div>PyMOL is incredibly useful because of its flexibility. Almost any setting can be tweaked to give you the ability to make your scenes appear just as you want. Each command usually comes with one or more settings. For example, the [[ray]] command comes with '''50''' settings!<br /> <br /> Below you will find the list of all known settings (as of this writing). Settings are added all the time, so this list should be updated somehow. Also, see all '''[[:Category:Settings|documented settings]]'''.<br /> <br /> If you feel like documenting them, and what they do, feel free.<br /> <br /> [[active_selections]]<br /> [[all_states]]<br /> [[ambient]]<br /> [[angle_color]]<br /> [[angle_label_position]]<br /> [[angle_size]]<br /> [[animation]]<br /> [[animation_duration]]<br /> [[antialias]]<br /> [[async_builds]]<br /> [[ati_bugs]]<br /> [[atom_name_wildcard]]<br /> [[auto_classify_atoms]]<br /> [[auto_color]]<br /> [[auto_copy_images]]<br /> [[auto_defer_builds]]<br /> [[auto_dss]]<br /> [[auto_hide_selections]]<br /> [[auto_indicate_flags]]<br /> [[auto_number_selections]]<br /> [[auto_remove_hydrogens]]<br /> [[auto_rename_duplicate_objects]]<br /> [[auto_sculpt]]<br /> [[auto_show_lines]]<br /> [[auto_show_nonbonded]]<br /> [[auto_show_selections]]<br /> [[auto_show_spheres]]<br /> [[auto_zoom]]<br /> [[backface_cull]]<br /> [[batch_prefix]]<br /> [[bg_rgb]]<br /> [[bonding_vdw_cutoff]]<br /> [[button_mode]]<br /> [[button_mode_name]]<br /> [[cache_display]]<br /> [[cache_frames]]<br /> [[cache_max]]<br /> [[cache_memory]]<br /> [[cache_mode]]<br /> [[cartoon_color]]<br /> [[cartoon_cylindrical_helices]]<br /> [[cartoon_debug]]<br /> [[cartoon_discrete_colors]]<br /> [[cartoon_dumbbell_length]]<br /> [[cartoon_dumbbell_radius]]<br /> [[cartoon_dumbbell_width]]<br /> [[cartoon_fancy_helices]]<br /> [[cartoon_fancy_sheets]]<br /> [[cartoon_flat_cycles]]<br /> [[cartoon_flat_sheets]]<br /> [[cartoon_helix_radius]]<br /> [[cartoon_highlight_color]]<br /> [[cartoon_ladder_color]]<br /> [[cartoon_ladder_mode]]<br /> [[cartoon_ladder_radius]]<br /> [[cartoon_loop_cap]]<br /> [[cartoon_loop_quality]]<br /> [[cartoon_loop_radius]]<br /> [[cartoon_nucleic_acid_color]]<br /> [[cartoon_nucleic_acid_mode]]<br /> [[cartoon_oval_length]]<br /> [[cartoon_oval_quality]]<br /> [[cartoon_oval_width]]<br /> [[cartoon_power]]<br /> [[cartoon_power_b]]<br /> [[cartoon_putty_quality]]<br /> [[cartoon_putty_radius]]<br /> [[cartoon_putty_range]]<br /> [[cartoon_putty_scale_max]]<br /> [[cartoon_putty_scale_min]]<br /> [[cartoon_putty_scale_power]]<br /> [[cartoon_putty_transform]]<br /> [[cartoon_rect_length]]<br /> [[cartoon_rect_width]]<br /> [[cartoon_refine]]<br /> [[cartoon_refine_normals]]<br /> [[cartoon_refine_tips]]<br /> [[cartoon_ring_color]]<br /> [[cartoon_ring_finder]]<br /> [[cartoon_ring_mode]]<br /> [[cartoon_ring_radius]]<br /> [[cartoon_ring_transparency]]<br /> [[cartoon_ring_width]]<br /> [[cartoon_round_helices]]<br /> [[cartoon_sampling]]<br /> [[cartoon_side_chain_helper]]<br /> [[cartoon_smooth_cycles]]<br /> [[cartoon_smooth_first]]<br /> [[cartoon_smooth_last]]<br /> [[cartoon_smooth_loops]]<br /> [[cartoon_throw]]<br /> [[cartoon_trace_atoms]]<br /> [[cartoon_transparency]]<br /> [[cartoon_tube_cap]]<br /> [[cartoon_tube_quality]]<br /> [[cartoon_tube_radius]]<br /> [[cavity_cull]]<br /> [[cgo_dot_radius]]<br /> [[cgo_dot_width]]<br /> [[cgo_ellipsoid_quality]]<br /> [[cgo_line_radius]]<br /> [[cgo_line_width]]<br /> [[cgo_ray_width_scale]]<br /> [[cgo_sphere_quality]]<br /> [[cgo_transparency]]<br /> [[clamp_colors]]<br /> [[cone_quality]]<br /> [[connect_bonded]]<br /> [[connect_cutoff]]<br /> [[connect_mode]]<br /> [[coulomb_cutoff]]<br /> [[coulomb_dielectric]]<br /> [[coulomb_units_factor]]<br /> [[cull_spheres]]<br /> [[dash_color]]<br /> [[dash_gap]]<br /> [[dash_length]]<br /> [[dash_radius]]<br /> [[dash_round_ends]]<br /> [[dash_width]]<br /> [[debug_pick]]<br /> [[defer_builds_mode]]<br /> [[defer_updates]]<br /> [[depth_cue]]<br /> [[dihedral_color]]<br /> [[dihedral_label_position]]<br /> [[dihedral_size]]<br /> [[direct]]<br /> [[dist_counter]]<br /> [[distance_exclusion]]<br /> [[dot_color]]<br /> [[dot_density]]<br /> [[dot_hydrogens]]<br /> [[dot_lighting]]<br /> [[dot_mode]]<br /> [[dot_normals]]<br /> [[dot_radius]]<br /> [[dot_solvent]]<br /> [[dot_width]]<br /> [[draw_frames]]<br /> [[editor_auto_dihedral]]<br /> [[editor_auto_origin]]<br /> [[editor_label_fragments]]<br /> [[ellipsoid_color]]<br /> [[ellipsoid_probability]]<br /> [[ellipsoid_quality]]<br /> [[ellipsoid_scale]]<br /> [[ellipsoid_transparency]]<br /> [[fast_idle]]<br /> [[fetch_path]]<br /> [[field_of_view]]<br /> [[fit_iterations]]<br /> [[fit_tolerance]]<br /> [[float_labels]]<br /> [[fog]]<br /> [[fog_start]]<br /> [[frame]]<br /> [[full_screen]]<br /> [[gamma]]<br /> [[gaussian_b_adjust]]<br /> [[gaussian_b_floor]]<br /> [[gaussian_resolution]]<br /> [[geometry_export_mode]]<br /> [[gl_ambient]]<br /> [[gradient_max_length]]<br /> [[gradient_min_length]]<br /> [[gradient_min_slope]]<br /> [[gradient_normal_min_dot]]<br /> [[gradient_spacing]]<br /> [[gradient_step_size]]<br /> [[gradient_symmetry]]<br /> [[grid_max]]<br /> [[grid_mode]]<br /> [[grid_slot]]<br /> [[group_arrow_prefix]]<br /> [[group_auto_mode]]<br /> [[group_full_member_names]]<br /> [[h_bond_cone]]<br /> [[h_bond_cutoff_center]]<br /> [[h_bond_cutoff_edge]]<br /> [[h_bond_exclusion]]<br /> [[h_bond_from_proton]]<br /> [[h_bond_max_angle]]<br /> [[h_bond_power_a]]<br /> [[h_bond_power_b]]<br /> [[half_bonds]]<br /> [[hash_max]]<br /> [[hide_long_bonds]]<br /> [[hide_underscore_names]]<br /> [[idle_delay]]<br /> [[ignore_case]]<br /> [[ignore_pdb_segi]]<br /> [[image_copy_always]]<br /> [[image_dots_per_inch]]<br /> [[internal_feedback]]<br /> [[internal_gui]]<br /> [[internal_gui_control_size]]<br /> [[internal_gui_mode]]<br /> [[internal_gui_width]]<br /> [[internal_prompt]]<br /> [[isomesh_auto_state]]<br /> [[label_angle_digits]]<br /> [[label_color]]<br /> [[label_digits]]<br /> [[label_dihedral_digits]]<br /> [[label_distance_digits]]<br /> [[label_font_id]]<br /> [[label_outline_color]]<br /> [[label_position]]<br /> [[label_shadow_mode]]<br /> [[label_size]]<br /> [[legacy_mouse_zoom]]<br /> [[legacy_vdw_radii]]<br /> [[light]]<br /> [[light2]]<br /> [[light3]]<br /> [[light4]]<br /> [[light5]]<br /> [[light6]]<br /> [[light7]]<br /> [[light8]]<br /> [[light9]]<br /> [[light_count]]<br /> [[line_color]]<br /> [[line_radius]]<br /> [[line_smooth]]<br /> [[line_stick_helper]]<br /> [[line_width]]<br /> [[log_box_selections]]<br /> [[log_conformations]]<br /> [[logging]]<br /> [[map_auto_expand_sym]]<br /> [[matrix_mode]]<br /> [[max_threads]]<br /> [[max_triangles]]<br /> [[mesh_carve_cutoff]]<br /> [[mesh_carve_selection]]<br /> [[mesh_carve_state]]<br /> [[mesh_clear_cutoff]]<br /> [[mesh_clear_selection]]<br /> [[mesh_clear_state]]<br /> [[mesh_color]]<br /> [[mesh_cutoff]]<br /> [[mesh_grid_max]]<br /> [[mesh_lighting]]<br /> [[mesh_mode]]<br /> [[mesh_negative_color]]<br /> [[mesh_negative_visible]]<br /> [[mesh_normals]]<br /> [[mesh_quality]]<br /> [[mesh_radius]]<br /> [[mesh_skip]]<br /> [[mesh_solvent]]<br /> [[mesh_type]]<br /> [[mesh_width]]<br /> [[min_mesh_spacing]]<br /> [[moe_separate_chains]]<br /> [[mouse_grid]]<br /> [[mouse_limit]]<br /> [[mouse_restart_movie_delay]]<br /> [[mouse_scale]]<br /> [[mouse_selection_mode]]<br /> [[mouse_wheel_scale]]<br /> [[movie_animate_by_frame]]<br /> [[movie_delay]]<br /> [[movie_fps]]<br /> [[movie_loop]]<br /> [[movie_rock]]<br /> [[multiplex]]<br /> [[no_idle]]<br /> [[nonbonded_size]]<br /> [[nonbonded_transparency]]<br /> [[normal_workaround]]<br /> [[normalize_ccp4_maps]]<br /> [[normalize_grd_maps]]<br /> [[normalize_o_maps]]<br /> [[nvidia_bugs]]<br /> [[opaque_background]]<br /> [[orthoscopic]]<br /> [[overlay]]<br /> [[overlay_lines]]<br /> [[pdb_conect_all]]<br /> [[pdb_discrete_chains]]<br /> [[pdb_echo_tags]]<br /> [[pdb_formal_charges]]<br /> [[pdb_hetatm_guess_valences]]<br /> [[pdb_hetatm_sort]]<br /> [[pdb_honor_model_number]]<br /> [[pdb_insertions_go_first]]<br /> [[pdb_insure_orthogonal]]<br /> [[pdb_literal_names]]<br /> [[pdb_no_end_record]]<br /> [[pdb_reformat_names_mode]]<br /> [[pdb_retain_ids]]<br /> [[pdb_standard_order]]<br /> [[pdb_truncate_residue_name]]<br /> [[pdb_unbond_cations]]<br /> [[pdb_use_ter_records]]<br /> [[pickable]]<br /> [[png_file_gamma]]<br /> [[png_screen_gamma]]<br /> [[power]]<br /> [[pqr_no_chain_id]]<br /> [[presentation]]<br /> [[presentation_auto_quit]]<br /> [[presentation_auto_start]]<br /> [[presentation_mode]]<br /> [[preserve_chempy_ids]]<br /> [[pymol_space_max_blue]]<br /> [[pymol_space_max_green]]<br /> [[pymol_space_max_red]]<br /> [[pymol_space_min_factor]]<br /> [[raise_exceptions]]<br /> [[ramp_blend_nearby_colors]]<br /> [[rank_assisted_sorts]]<br /> [[ray_blend_blue]]<br /> [[ray_blend_colors]]<br /> [[ray_blend_green]]<br /> [[ray_blend_red]]<br /> [[ray_clip_shadows]]<br /> [[ray_color_ramps]]<br /> [[ray_default_renderer]]<br /> [[ray_direct_shade]]<br /> [[ray_hint_camera]]<br /> [[ray_hint_shadow]]<br /> [[ray_improve_shadows]]<br /> [[ray_interior_color]]<br /> [[ray_interior_mode]]<br /> [[ray_interior_reflect]]<br /> [[ray_interior_shadows]]<br /> [[ray_interior_texture]]<br /> [[ray_label_specular]]<br /> [[ray_legacy_lighting]]<br /> [[ray_max_passes]]<br /> [[ray_opaque_background]]<br /> [[ray_orthoscopic]]<br /> [[ray_oversample_cutoff]]<br /> [[ray_pixel_scale]]<br /> [[ray_scatter]]<br /> [[ray_shadow]]<br /> [[ray_shadow_decay_factor]]<br /> [[ray_shadow_decay_range]]<br /> [[ray_shadow_fudge]]<br /> [[ray_shadows]]<br /> [[ray_spec_local]]<br /> [[ray_texture]]<br /> [[ray_texture_settings]]<br /> [[ray_trace_color]]<br /> [[ray_trace_depth_factor]]<br /> [[ray_trace_disco_factor]]<br /> [[ray_trace_fog]]<br /> [[ray_trace_fog_start]]<br /> [[ray_trace_frames]]<br /> [[ray_trace_gain]]<br /> [[ray_trace_mode]]<br /> [[ray_trace_persist_cutoff]]<br /> [[ray_trace_slope_factor]]<br /> [[ray_trace_trans_cutoff]]<br /> [[ray_transparency_contrast]]<br /> [[ray_transparency_oblique]]<br /> [[ray_transparency_oblique_power]]<br /> [[ray_transparency_shadows]]<br /> [[ray_transparency_spec_cut]]<br /> [[ray_transparency_specular]]<br /> [[ray_triangle_fudge]]<br /> [[reflect]]<br /> [[reflect_power]]<br /> [[retain_order]]<br /> [[ribbon_color]]<br /> [[ribbon_nucleic_acid_mode]]<br /> [[ribbon_power]]<br /> [[ribbon_power_b]]<br /> [[ribbon_radius]]<br /> [[ribbon_sampling]]<br /> [[ribbon_side_chain_helper]]<br /> [[ribbon_smooth]]<br /> [[ribbon_throw]]<br /> [[ribbon_trace_atoms]]<br /> [[ribbon_width]]<br /> [[robust_logs]]<br /> [[rock]]<br /> [[rock_delay]]<br /> [[roving_byres]]<br /> [[roving_cartoon]]<br /> [[roving_delay]]<br /> [[roving_detail]]<br /> [[roving_isomesh]]<br /> [[roving_isosurface]]<br /> [[roving_labels]]<br /> [[roving_lines]]<br /> [[roving_map1_level]]<br /> [[roving_map1_name]]<br /> [[roving_map2_level]]<br /> [[roving_map2_name]]<br /> [[roving_map3_level]]<br /> [[roving_map3_name]]<br /> [[roving_nb_spheres]]<br /> [[roving_nonbonded]]<br /> [[roving_origin]]<br /> [[roving_origin_z]]<br /> [[roving_origin_z_cushion]]<br /> [[roving_polar_contacts]]<br /> [[roving_polar_cutoff]]<br /> [[roving_ribbon]]<br /> [[roving_selection]]<br /> [[roving_spheres]]<br /> [[roving_sticks]]<br /> [[scene_animation]]<br /> [[scene_animation_duration]]<br /> [[scene_buttons]]<br /> [[scene_buttons_mode]]<br /> [[scene_current_name]]<br /> [[scene_loop]]<br /> [[scene_restart_movie_delay]]<br /> [[scenes_changed]]<br /> [[sculpt_angl_weight]]<br /> [[sculpt_auto_center]]<br /> [[sculpt_avd_excl]]<br /> [[sculpt_avd_gap]]<br /> [[sculpt_avd_range]]<br /> [[sculpt_avd_weight]]<br /> [[sculpt_bond_weight]]<br /> [[sculpt_field_mask]]<br /> [[sculpt_hb_overlap]]<br /> [[sculpt_hb_overlap_base]]<br /> [[sculpt_line_weight]]<br /> [[sculpt_max_max]]<br /> [[sculpt_max_min]]<br /> [[sculpt_max_scale]]<br /> [[sculpt_max_weight]]<br /> [[sculpt_memory]]<br /> [[sculpt_min_max]]<br /> [[sculpt_min_min]]<br /> [[sculpt_min_scale]]<br /> [[sculpt_min_weight]]<br /> [[sculpt_nb_interval]]<br /> [[sculpt_plan_weight]]<br /> [[sculpt_pyra_weight]]<br /> [[sculpt_tors_tolerance]]<br /> [[sculpt_tors_weight]]<br /> [[sculpt_tri_max]]<br /> [[sculpt_tri_min]]<br /> [[sculpt_tri_mode]]<br /> [[sculpt_tri_scale]]<br /> [[sculpt_tri_weight]]<br /> [[sculpt_vdw_scale]]<br /> [[sculpt_vdw_scale14]]<br /> [[sculpt_vdw_vis_max]]<br /> [[sculpt_vdw_vis_mid]]<br /> [[sculpt_vdw_vis_min]]<br /> [[sculpt_vdw_vis_mode]]<br /> [[sculpt_vdw_weight]]<br /> [[sculpt_vdw_weight14]]<br /> [[sculpting]]<br /> [[sculpting_cycles]]<br /> [[sdof_drag_scale]]<br /> [[secondary_structure]]<br /> [[security]]<br /> [[sel_counter]]<br /> [[selection_overlay]]<br /> [[selection_round_points]]<br /> [[selection_visible_only]]<br /> [[selection_width]]<br /> [[selection_width_max]]<br /> [[selection_width_scale]]<br /> [[seq_view]]<br /> [[seq_view_alignment]]<br /> [[seq_view_color]]<br /> [[seq_view_discrete_by_state]]<br /> [[seq_view_fill_char]]<br /> [[seq_view_fill_color]]<br /> [[seq_view_format]]<br /> [[seq_view_label_color]]<br /> [[seq_view_label_mode]]<br /> [[seq_view_label_spacing]]<br /> [[seq_view_label_start]]<br /> [[seq_view_location]]<br /> [[seq_view_overlay]]<br /> [[seq_view_unaligned_color]]<br /> [[seq_view_unaligned_mode]]<br /> [[session_cache_optimize]]<br /> [[session_changed]]<br /> [[session_compression]]<br /> [[session_file]]<br /> [[session_migration]]<br /> [[session_version_check]]<br /> [[shininess]]<br /> [[show_alpha_checker]]<br /> [[show_progress]]<br /> [[simplify_display_lists]]<br /> [[single_image]]<br /> [[slice_dynamic_grid]]<br /> [[slice_dynamic_grid_resolution]]<br /> [[slice_grid]]<br /> [[slice_height_map]]<br /> [[slice_height_scale]]<br /> [[slice_track_camera]]<br /> [[slow_idle]]<br /> [[smooth_color_triangle]]<br /> [[solvent_radius]]<br /> [[spec_count]]<br /> [[spec_direct]]<br /> [[spec_direct_power]]<br /> [[spec_power]]<br /> [[spec_reflect]]<br /> [[specular]]<br /> [[specular_intensity]]<br /> [[sphere_color]]<br /> [[sphere_mode]]<br /> [[sphere_point_max_size]]<br /> [[sphere_point_size]]<br /> [[sphere_quality]]<br /> [[sphere_scale]]<br /> [[sphere_solvent]]<br /> [[sphere_transparency]]<br /> [[spheroid_fill]]<br /> [[spheroid_scale]]<br /> [[spheroid_smooth]]<br /> [[ss_helix_phi_exclude]]<br /> [[ss_helix_phi_include]]<br /> [[ss_helix_phi_target]]<br /> [[ss_helix_psi_exclude]]<br /> [[ss_helix_psi_include]]<br /> [[ss_helix_psi_target]]<br /> [[ss_strand_phi_exclude]]<br /> [[ss_strand_phi_include]]<br /> [[ss_strand_phi_target]]<br /> [[ss_strand_psi_exclude]]<br /> [[ss_strand_psi_include]]<br /> [[ss_strand_psi_target]]<br /> [[state]]<br /> [[static_singletons]]<br /> [[stereo]]<br /> [[stereo_angle]]<br /> [[stereo_double_pump_mono]]<br /> [[stereo_mode]]<br /> [[stereo_shift]]<br /> [[stick_ball]]<br /> [[stick_ball_ratio]]<br /> [[stick_color]]<br /> [[stick_fixed_radius]]<br /> [[stick_nub]]<br /> [[stick_overlap]]<br /> [[stick_quality]]<br /> [[stick_radius]]<br /> [[stick_transparency]]<br /> [[stick_valence_scale]]<br /> [[stop_on_exceptions]]<br /> [[suppress_hidden]]<br /> [[surface_best]]<br /> [[surface_carve_cutoff]]<br /> [[surface_carve_normal_cutoff]]<br /> [[surface_carve_selection]]<br /> [[surface_carve_state]]<br /> [[surface_cavity_cutoff]]<br /> [[surface_cavity_mode]]<br /> [[surface_cavity_radius]]<br /> [[surface_circumscribe]]<br /> [[surface_clear_cutoff]]<br /> [[surface_clear_selection]]<br /> [[surface_clear_state]]<br /> [[surface_color]]<br /> [[surface_debug]]<br /> [[surface_miserable]]<br /> [[surface_mode]]<br /> [[surface_negative_color]]<br /> [[surface_negative_visible]]<br /> [[surface_normal]]<br /> [[surface_optimize_subsets]]<br /> [[surface_poor]]<br /> [[surface_proximity]]<br /> [[surface_quality]]<br /> [[surface_ramp_above_mode]]<br /> [[surface_solvent]]<br /> [[surface_trim_cutoff]]<br /> [[surface_trim_factor]]<br /> [[surface_type]]<br /> [[suspend_updates]]<br /> [[swap_dsn6_bytes]]<br /> [[sweep_angle]]<br /> [[sweep_mode]]<br /> [[sweep_phase]]<br /> [[sweep_speed]]<br /> [[test1]]<br /> [[test2]]<br /> [[text]]<br /> [[texture_fonts]]<br /> [[trace_atoms_mode]]<br /> [[transparency]]<br /> [[transparency_global_sort]]<br /> [[transparency_mode]]<br /> [[transparency_picking_mode]]<br /> [[triangle_max_passes]]<br /> [[trim_dots]]<br /> [[two_sided_lighting]]<br /> [[use_display_lists]]<br /> [[valence]]<br /> [[valence_default]]<br /> [[valence_size]]<br /> [[validate_object_names]]<br /> [[virtual_trackball]]<br /> [[wildcard]]<br /> [[wizard_prompt_mode]]<br /> [[wrap_output]]<br /> <br /> [[Category:Settings|All Settings]]</div>

Saper https://wiki.pymol.org/index.php?title=User:Saper&diff=3065 2010-06-10T01:40:26Z

<p>Saper: </p> <hr /> <div>== Mark A. Saper, Ph.D. ==<br /> <br /> I'm a structural biologist at the University of Michigan and a great fan of PyMol since its inception. Also a Mac OS X enthusiast.<br /> <br /> *[http://biop.lsa.umich.edu/111new-page.aspx Saper research interest page]<br /> *Saper Lab [http://www.umich.edu/~saper web site] (incomplete)</div>

Saper https://wiki.pymol.org/index.php?title=User:Saper&diff=3064 2010-06-10T01:39:32Z

<p>Saper: </p> <hr /> <div>== Mark A. Saper, Ph.D. ==<br /> <br /> I'm a structural biologist at the University of Michigan and a great fan of PyMol since its inception. Also a Mac OS X enthusiast.<br /> <br /> *Saper research interest page [http://biop.lsa.umich.edu/111new-page.aspx]<br /> *Saper Lab [http://www.umich.edu/~saper web site] (incomplete)</div>

Saper https://wiki.pymol.org/index.php?title=User:Saper&diff=3063 2010-06-10T01:36:31Z

<p>Saper: Revert to page before spam</p> <hr /> <div>== Mark A. Saper, Ph.D. ==<br /> <br /> I'm a structural biologist at the University of Michigan and a great fan of PyMol since its inception. Also a Mac OS X enthusiast.<br /> <br /> *[http://photon.biop.umich.edu/FMPro?-db=brd_fac.fp5&amp;-lay=main&amp;ref_name=sapermark&amp;-format=brd_fac/brd_fac_desc.htm&amp;-find Saper research interest page]<br /> *Saper Lab [http://www.umich.edu/~saper web site] (incomplete)</div>

Saper https://wiki.pymol.org/index.php?title=User_talk:Inchoate&diff=10793 2010-03-10T17:22:34Z

<p>Saper: /* Section &quot;file is not of required architecture&quot; */</p> <hr /> <div>Jason,<br /> Conserning the Kabsch alogrithm.... Can you take two sets of vectors with different numbers in each set and have it loop over the larger set?<br /> <br /> For instance,<br /> I have CA and CB positions for 4 residues (residues aren't sequential), could I find the optimal RMSD between the 4 residue CA_CB set and a another protein (well, it's own CA_CB set) ?<br /> <br /> I haven't looked at the code, but I figured you are more familiar with it.<br /> <br /> Thanks,<br /> Dan<br /> <br /> ----<br /> <br /> Hello, I'm thinking of making changes to the GalleryImage template. I wanted to check with you about these changes before I made them:<br /> &lt;ul&gt;<br /> &lt;li&gt; I feel that the description column is unnecessary. Putting the description below the image is probably good enough. Also, for a table which stretches horizontally, in which horizontal screen space is very valuable, an extra column for this seems like a waste.&lt;/li&gt;<br /> &lt;li&gt; Does each row have to be centered? Maybe left aligning the rows is better.&lt;/li&gt;<br /> &lt;li&gt; A divider between each entry would be nice.&lt;/li&gt;<br /> &lt;li&gt; I understand why you make the GalleryImage template this way, but maybe an overhaul is necessary... Long 'What to Type' sections can easily make an entry cumbersome (just look at mine).&lt;/li&gt;<br /> &lt;li&gt; For visual pretty-ness, maybe having fixed widths for the sections? (Course this could lead to problems...)&lt;/li&gt;&lt;/ul&gt;<br /> BTW, thanks for making the GalleryImage template. I especially like the 'See Also' section, as I wouldn't have thought of adding it...&lt;br&gt;--[[User:Ojganesh|Ojganesh]] 15:01, 25 August 2008 (CDT)<br /> <br /> ----<br /> <br /> Hey again,<br /> I like the Covers section of the wiki! Good addition! You may want to black out the address labels on the magazine covers...&lt;br&gt;--[[User:Ojganesh|Ojganesh]] 08:46, 8 September 2008 (CDT)<br /> <br /> ----<br /> <br /> Hi Jason,<br /> <br /> Thanks for checking out ColorByRMSD. As for the problems, here is my take on some of the things:<br /> <br /> 1. You are right, there is no need to multiply the new b-factors (rmsd) by 10, as Pymol will them scale automatically.<br /> <br /> 2. The properties of the &quot;aln&quot; object as returned by &quot;super&quot; are not the same as returned by &quot;align&quot; !!! Go figure!<br /> <br /> 3. Reverting to &quot;align&quot; for generating the 'aln&quot; object results in way faster execution time. Not surprising, as the lengths of the &quot;stored.alnAres&quot; and &quot;stored.alnBres&quot; arrays is MUCH bigger if stuffed by contents from &quot;super&quot;'s &quot;aln&quot;... :-)) But this leaves us to deal with the brain-dead &quot;align&quot; command, as I commented in my original script.<br /> <br /> 4. I think all the points you make regarding keeping user's original objects untouched etc. are valid and are essential to making this a generic script... I barely grok python (you can tell!) and can certainly use all the help I can get from the gurus! Thanks!!<br /> <br /> 5. Please do re-run the updated script (still based off my original code) to see the points I talk about above.<br /> <br /> 6. One more thing that you have noticed indirectly: What about the b-factors of residues that are not a part of the &quot;aln&quot; object? They will corrupt the coloring by b-factor... right? Oh, and in the final command, in the original script, I must color the final object by selecting &quot;objectname and polymer&quot; for b-factor coloring or else the b-factors of solvents/non-protein atoms corrupt the coloring. I updated the code to reflect this.<br /> <br /> --[[User:Shiven|shiven]] 03:49, 15 July 2009 (UTC)<br /> <br /> == Section &quot;file is not of required architecture&quot; ==<br /> <br /> Hi Jason,<br /> <br /> I think you added the section &quot;file is not of required architecture&quot; to the [[cealign]] page. I think this would be better placed back where the Mac installation is discussed because it alerts of a different symptom of the same problem. <br /> <br /> Also, I think a better work-around that doesn't mess with the system files would be this.<br /> <br /> &lt;source lang=&quot;bash&quot;&gt;<br /> cd [pathname]/cealign-0.9<br /> ln -s /usr/bin/gcc-4.0 ./gcc<br /> ln -s /usr/bin/g++-4.0 ./g++<br /> set oldpath= $path<br /> set path=( . $path )<br /> sudo /sw/bin/python setup.py install<br /> set path=oldpath<br /> &lt;/source&gt;<br /> <br /> If this is reasonable, I can make the changes.<br /> &lt;br&gt;Regards, Mark ([[user:saper]]) 3/10/2010</div>

Saper https://wiki.pymol.org/index.php?title=User_talk:Inchoate&diff=10792 2010-03-10T17:22:12Z

<p>Saper: /* Section &quot;file is not of required architecture&quot; */ new section</p> <hr /> <div>Jason,<br /> Conserning the Kabsch alogrithm.... Can you take two sets of vectors with different numbers in each set and have it loop over the larger set?<br /> <br /> For instance,<br /> I have CA and CB positions for 4 residues (residues aren't sequential), could I find the optimal RMSD between the 4 residue CA_CB set and a another protein (well, it's own CA_CB set) ?<br /> <br /> I haven't looked at the code, but I figured you are more familiar with it.<br /> <br /> Thanks,<br /> Dan<br /> <br /> ----<br /> <br /> Hello, I'm thinking of making changes to the GalleryImage template. I wanted to check with you about these changes before I made them:<br /> &lt;ul&gt;<br /> &lt;li&gt; I feel that the description column is unnecessary. Putting the description below the image is probably good enough. Also, for a table which stretches horizontally, in which horizontal screen space is very valuable, an extra column for this seems like a waste.&lt;/li&gt;<br /> &lt;li&gt; Does each row have to be centered? Maybe left aligning the rows is better.&lt;/li&gt;<br /> &lt;li&gt; A divider between each entry would be nice.&lt;/li&gt;<br /> &lt;li&gt; I understand why you make the GalleryImage template this way, but maybe an overhaul is necessary... Long 'What to Type' sections can easily make an entry cumbersome (just look at mine).&lt;/li&gt;<br /> &lt;li&gt; For visual pretty-ness, maybe having fixed widths for the sections? (Course this could lead to problems...)&lt;/li&gt;&lt;/ul&gt;<br /> BTW, thanks for making the GalleryImage template. I especially like the 'See Also' section, as I wouldn't have thought of adding it...&lt;br&gt;--[[User:Ojganesh|Ojganesh]] 15:01, 25 August 2008 (CDT)<br /> <br /> ----<br /> <br /> Hey again,<br /> I like the Covers section of the wiki! Good addition! You may want to black out the address labels on the magazine covers...&lt;br&gt;--[[User:Ojganesh|Ojganesh]] 08:46, 8 September 2008 (CDT)<br /> <br /> ----<br /> <br /> Hi Jason,<br /> <br /> Thanks for checking out ColorByRMSD. As for the problems, here is my take on some of the things:<br /> <br /> 1. You are right, there is no need to multiply the new b-factors (rmsd) by 10, as Pymol will them scale automatically.<br /> <br /> 2. The properties of the &quot;aln&quot; object as returned by &quot;super&quot; are not the same as returned by &quot;align&quot; !!! Go figure!<br /> <br /> 3. Reverting to &quot;align&quot; for generating the 'aln&quot; object results in way faster execution time. Not surprising, as the lengths of the &quot;stored.alnAres&quot; and &quot;stored.alnBres&quot; arrays is MUCH bigger if stuffed by contents from &quot;super&quot;'s &quot;aln&quot;... :-)) But this leaves us to deal with the brain-dead &quot;align&quot; command, as I commented in my original script.<br /> <br /> 4. I think all the points you make regarding keeping user's original objects untouched etc. are valid and are essential to making this a generic script... I barely grok python (you can tell!) and can certainly use all the help I can get from the gurus! Thanks!!<br /> <br /> 5. Please do re-run the updated script (still based off my original code) to see the points I talk about above.<br /> <br /> 6. One more thing that you have noticed indirectly: What about the b-factors of residues that are not a part of the &quot;aln&quot; object? They will corrupt the coloring by b-factor... right? Oh, and in the final command, in the original script, I must color the final object by selecting &quot;objectname and polymer&quot; for b-factor coloring or else the b-factors of solvents/non-protein atoms corrupt the coloring. I updated the code to reflect this.<br /> <br /> --[[User:Shiven|shiven]] 03:49, 15 July 2009 (UTC)<br /> <br /> == Section &quot;file is not of required architecture&quot; ==<br /> <br /> Hi Jason,<br /> <br /> I think you added the section &quot;file is not of required architecture&quot; to the [[cealign]] page. I think this would be better placed back where the Mac installation is discussed because it alerts of a different symptom of the same problem. <br /> <br /> Also, I think a better work-around that doesn't mess with the system files would be this.<br /> <br /> &lt;source lang=&quot;bash&quot;&gt;<br /> cd [pathname]/cealign-0.9<br /> ln -s /usr/bin/gcc-4.0 ./gcc<br /> ln -s /usr/bin/g++-4.0 ./g++<br /> set oldpath= $path<br /> set path=( . $path )<br /> sudo /sw/bin/python setup.py install<br /> set path=oldpath<br /> &lt;/source&gt;<br /> <br /> If this is reasonable, I can make the changes.<br /> &lt;br&gt;Regards, Mark ([[user:saper]])</div>

Saper https://wiki.pymol.org/index.php?title=Label_font_id&diff=7822 2010-02-11T00:05:34Z

<p>Saper: Fixed Unicdoe</p> <hr /> <div>== Overview ==<br /> Set which fonts PyMol uses to render labels. Font IDs 5&amp;mdash;14 are normal fonts, while 15 and 16 are for unicode fonts (and can support many more characters).<br /> <br /> == Syntax ==<br /> &lt;source lang=&quot;python&quot;&gt;<br /> set label_font_id, 10 # use font no. 10<br /> set label_font_id, 11 # use font no. 11<br /> set label_font_id, 12 # use font no. 12<br /> &lt;/source&gt;<br /> <br /> == UTF-8 Fonts ==<br /> [[Image:New_fonts.jpeg|thumb|New fonts in PyMol. Notice the alpha and beta characters.]]<br /> <br /> Newer versions support UTF8 fonts; use '''label_font_id''' from above to 15 or 16. The good news about the UTF8 fonts is that they support the alpha and beta characters. (See image.)<br /> <br /> Here's some example code for the image at right:<br /> &lt;source lang=&quot;python&quot;&gt;<br /> # roman<br /> set label_font_id, 15<br /> set label_shadow_mode, 3<br /> label 5/CA, &quot;\316\261-Helix&quot;<br /> label 10/CA, &quot;\316\262-Sheet&quot;<br /> <br /> # italic<br /> set label_font_id, 16<br /> <br /> # make bigger<br /> set label_size, 50<br /> &lt;/source&gt;<br /> <br /> ==Unicode Fonts==<br /> [[Image:Font_ex.png|300px|thumb|right|Notice the Angstrom and superscript 2 characters. You can add other characters as well.]]<br /> <br /> PyMOL gives you the flexibility to use encoded unicode fonts. This allows us to insert various symbols, like the symbol used for Angstrom. Here are the steps to insert a character from the unicode character set.<br /> <br /> * Find the code for your character at [http://www.unicode.org/charts Unicode Charts]. The Angstrom character, &lt;math&gt;\textrm{\AA}&lt;/math&gt; is u&quot;\u00c5&quot; and &lt;math&gt;\pm&lt;/math&gt; is u&quot;\u00b1&quot;.<br /> * Label the selection. For simple strings, just type the string in double quote, -- &quot;like this&quot; -- and append to the end of that .encode('utf-8') -- &quot;like this&quot;.encode('utf-8'). A working example is shown here,<br /> &lt;source lang=&quot;python&quot;&gt;<br /> # label residue 30 with &quot;4.1 Ang^2 +/- 0.65 Ang^2; see the image at right<br /> label i. 30, &quot;4.1&quot; + u&quot;\u00c5\u00b2 \u00b1 0.65 \u00c5\u00b2 &quot;.encode('utf-8')<br /> &lt;/source&gt;<br /> <br /> <br /> <br /> [[Category:Settings|Label font id]]<br /> [[Category:Labeling|Label font id]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10571 2005-08-19T04:29:17Z

<p>Saper: Fixed error in EXAMPLES</p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = new or modified object that will contain transformed coordinates<br /> * selection = selection of atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform_odb moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Please send questions or bug reports to Mark Saper, mailto:saper@umich.edu<br /> <br /> ===SOURCE===<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Main_Page&diff=4515 2005-08-02T18:10:59Z

<p>Saper: /* News */</p> <hr /> <div>== PyMol Wiki Home ==<br /> You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.<br /> <br /> We provide<br /> * updates on [http://pymol.sf.net PyMol]<br /> * a stable user-oriented documentation base<br /> * a thorough treatment of the PyMol program<br /> * feature-rich scripts for general PyMol use<br /> <br /> ==News==<br /> * PyMol gets some new features. PyMol 0.99beta07 added these commands for testing, check out the new <br /> # [[Draw]] command and,<br /> # [[Spheres]] Shader Spheres represenation<br /> * Also, [[Ray]] and [[Draw]] now show oversized images scaled into the viewport.<br /> <br /> * New [[Transform_odb]] script to transform coordinates with .odb file from O or LSQMAN<br /> <br /> == Links of Interest ==<br /> * [[TOPTOC|Top Level Table of Contents]]<br /> * [[:Category:FAQ|Frequently Asked Questions]] -- new!<br /> * [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something<br /> * [[:Category:Script Library| Script Library]] -- add one! (rTools info!)<br /> * [[:Category:Commands|PyMol Commands]] (&gt;130 documented!)<br /> * [[:Special:Allpages| All Pages]]<br /> * [[:Category:Plugins|Plugins]]<br /> * [[:Special:Categories| See All Categories]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10570 2005-08-02T17:52:15Z

<p>Saper: /* USAGE */</p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = new or modified object that will contain transformed coordinates<br /> * selection = selection of atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Please send questions or bug reports to Mark Saper, mailto:saper@umich.edu<br /> <br /> ===SOURCE===<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10569 2005-08-02T17:49:40Z

<p>Saper: </p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Please send questions or bug reports to Mark Saper, mailto:saper@umich.edu<br /> <br /> ===SOURCE===<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10568 2005-08-02T17:49:11Z

<p>Saper: </p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Please send questions or bug reports to Mark Saper, mailto:saper@umich.edu<br /> <br /> ===SOURCE===<br /> <br /> * Download<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10567 2005-08-02T04:25:30Z

<p>Saper: </p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Contact<br /> <br /> ===SOURCE===<br /> <br /> * Download<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb.py&diff=5708 2005-08-02T04:22:42Z

<p>Saper: </p> <hr /> <div>from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> <br /> #print theCurrLine[0]<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> <br /> # close the file<br /> theInFile.close ()<br /> #<br /> r = cmd.create ( name, selection)<br /> <br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10566 2005-08-02T04:21:54Z

<p>Saper: </p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Contact<br /> <br /> ===SOURCE===<br /> <br /> * Download [[transform_odb.py]]<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10565 2005-08-02T04:21:10Z

<p>Saper: </p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Contact<br /> <br /> ===[[SOURCE]]===<br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10564 2005-08-02T04:20:19Z

<p>Saper: Includes source</p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Contact<br /> <br /> ===SOURCE===<br /> &lt;source lang=&quot;python&quot;&gt;<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> &lt;/source&gt;<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10563 2005-08-02T04:17:47Z

<p>Saper: </p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> Contact<br /> <br /> ===Source===<br /> from pymol import cmd<br /> import pymol<br /> import os<br /> import re<br /> import string<br /> <br /> def __init__(self):<br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> # Creates a new object name from selection after transforming it with O-style matrix<br /> # found in matrix_file<br /> # Author: Mark Saper &lt;saper@umich.edu&gt;<br /> <br /> def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):<br /> <br /> # open the file for reading<br /> matrix_file = os.path.expanduser(matrix_file)<br /> matrix_file = os.path.expandvars(matrix_file)<br /> theInFile = open ( matrix_file,&quot;r&quot;)<br /> <br /> # what we'll store the results in<br /> theMatrix = []<br /> <br /> # read every line in the file and ...<br /> for theCurrLine in theInFile.readlines():<br /> if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):<br /> # if the line isn't blank, make a list of items seperated by tabs<br /> theNewRow = string.split (theCurrLine)<br /> # add it in the matrix<br /> theMatrix.extend ( theNewRow )<br /> <br /> # change matrix to pymol unsupported format<br /> <br /> theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],<br /> theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],<br /> theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], <br /> 0.0, 0.0, 0.0, 0.0 ]<br /> theMatrix = [ float(x) for x in theMatrix] <br /> <br /> # close the file<br /> theInFile.close ()<br /> <br /> r = cmd.create ( name, selection)<br /> r = cmd.transform_object( name, theMatrix, transpose=transpose)<br /> <br /> return r<br /> <br /> cmd.extend('transform_odb', transform_odb)<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10562 2005-08-02T04:13:19Z

<p>Saper: </p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Script Library|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Transform_odb&diff=10561 2005-08-02T04:11:42Z

<p>Saper: Initial version</p> <hr /> <div>===DESCRIPTION===<br /> &quot;transform_odb&quot; transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> ===USAGE===<br /> transform_odb name, (selection), matrix_file [, transpose]<br /> <br /> * name = object to contain transformed coordinates<br /> * selection = atoms to transform<br /> * matrix_file = file name or path of .odb file containing a transformation matrix data block<br /> * transpose (default 0]<br /> <br /> <br /> ===EXAMPLES===<br /> transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb<br /> <br /> ===USER COMMENTS===<br /> <br /> ===SEE ALSO===<br /> transform_selection, transform_object<br /> <br /> [[Category:Scripts|transform_odb]]</div>

Saper https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3871 2005-08-02T03:50:17Z

<p>Saper: </p> <hr /> <div>* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an &quot;O&quot;-style tranformation matrix file (.odb) written by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> * [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.<br /> <br /> * [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X<br /> <br /> * [[Show aromatics]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for aromatic residues displayed as green &quot;sticks&quot;. Usage: Save this as &quot;show_aromatics.pml&quot;, load your protein in PyMOL, and run the script (select &quot;Run&quot; from the &quot;File&quot; menu). (PyMOL script; TStout)<br /> <br /> * [[Show hydrophobics]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for hydrophobic residues displayed as orange &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Show charged]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Show hydrophilic]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for hydrophilic residues displayed as green &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])<br /> <br /> * [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.<br /> <br /> * [[CGO Text]] -- Creates a 3D-CGO text object.<br /> <br /> * [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).<br /> <br /> * [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).<br /> <br /> * [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').<br /> <br /> * [[Split Movement]] -- Moves two parts of one object into different directions.<br /> <br /> * [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.<br /> <br /> * [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.<br /> <br /> * [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).<br /> <br /> * [[grepset]] -- List all settings matching a given keyword. - ''by EHP''<br /> <br /> * [[disconnect]] -- unbond a single atom from its neighbors. - ''by EHP''<br /> <br /> * [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''<br /> <br /> * [[Measure Distance]] -- Measures the distance between two atoms (Python script).<br /> <br /> * [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.<br /> <br /> * [[Color Objects]] -- Colors all objects differently (Python script).<br /> <br /> * [[Key Wait]] -- Process key events in a Python script.<br /> <br /> * [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)<br /> <br /> * [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)<br /> <br /> * [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)<br /> <br /> * [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.<br /> <br /> * [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!<br /> <br /> * [[grepsel]] -- Make named selections using regular expressions (protein sequence).<br /> <br /> [[Category:Scripting|Script Library]]</div>

Saper https://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3870 2005-08-02T03:49:41Z

<p>Saper: Add new transform_odb command</p> <hr /> <div>* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an &quot;O&quot;-style tranformation matrix file output by &quot;O&quot; or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.<br /> <br /> * [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.<br /> <br /> * [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X<br /> <br /> * [[Show aromatics]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for aromatic residues displayed as green &quot;sticks&quot;. Usage: Save this as &quot;show_aromatics.pml&quot;, load your protein in PyMOL, and run the script (select &quot;Run&quot; from the &quot;File&quot; menu). (PyMOL script; TStout)<br /> <br /> * [[Show hydrophobics]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for hydrophobic residues displayed as orange &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Show charged]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Show hydrophilic]] -- This script will display a backbone &quot;worm&quot; for your protein, with all of the sidechains for hydrophilic residues displayed as green &quot;sticks&quot;. Usage: Same as &quot;show aromatics&quot;. (PyMOL script; TStout)<br /> <br /> * [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])<br /> <br /> * [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.<br /> <br /> * [[CGO Text]] -- Creates a 3D-CGO text object.<br /> <br /> * [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).<br /> <br /> * [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).<br /> <br /> * [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').<br /> <br /> * [[Split Movement]] -- Moves two parts of one object into different directions.<br /> <br /> * [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.<br /> <br /> * [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.<br /> <br /> * [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).<br /> <br /> * [[grepset]] -- List all settings matching a given keyword. - ''by EHP''<br /> <br /> * [[disconnect]] -- unbond a single atom from its neighbors. - ''by EHP''<br /> <br /> * [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''<br /> <br /> * [[Measure Distance]] -- Measures the distance between two atoms (Python script).<br /> <br /> * [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.<br /> <br /> * [[Color Objects]] -- Colors all objects differently (Python script).<br /> <br /> * [[Key Wait]] -- Process key events in a Python script.<br /> <br /> * [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)<br /> <br /> * [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)<br /> <br /> * [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)<br /> <br /> * [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.<br /> <br /> * [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!<br /> <br /> * [[grepsel]] -- Make named selections using regular expressions (protein sequence).<br /> <br /> [[Category:Scripting|Script Library]]</div>

Saper https://wiki.pymol.org/index.php?title=User:Saper&diff=3060 2005-02-17T05:17:08Z

<p>Saper: /* Saper Page */</p> <hr /> <div>== Mark A. Saper, Ph.D. ==<br /> <br /> I'm a structural biologist at the University of Michigan and a great fan of PyMol since its inception. Also a Mac OS X enthusiast.<br /> <br /> *[http://photon.biop.umich.edu/FMPro?-db=brd_fac.fp5&amp;-lay=main&amp;ref_name=sapermark&amp;-format=brd_fac/brd_fac_desc.htm&amp;-find Saper research interest page]<br /> *Saper Lab [http://www.umich.edu/~saper web site] (incomplete)</div>

Saper https://wiki.pymol.org/index.php?title=User:Saper&diff=3059 2005-02-17T05:16:11Z

<p>Saper: Mark Saper's Page</p> <hr /> <div>== Saper Page ==<br /> <br /> I'm a structural biologist at the University of Michigan and a great fan of PyMol since its inception. <br /> <br /> *[http://photon.biop.umich.edu/FMPro?-db=brd_fac.fp5&amp;-lay=main&amp;ref_name=sapermark&amp;-format=brd_fac/brd_fac_desc.htm&amp;-find Saper research interest page]<br /> *Saper Lab [http://www.umich.edu/~saper web site] (incomplete)</div>

Saper https://wiki.pymol.org/index.php?title=User:Saper&diff=3058 2005-02-17T05:10:48Z

<p>Saper: Mark Saper's Page</p> <hr /> <div><br /> == Saper Page ==<br /> <br /> <br /> I'm a structural biologist at the University of Michigan and a great fan of PyMol since its inception. <br /> <br /> <br /> *My [http://www.umich.edu/~biophys research interest page]<br /> *Lab web site (preliminary)</div>

Saper https://wiki.pymol.org/index.php?title=Talk:Main_Page&diff=349 2005-02-17T04:54:29Z

<p>Saper: User manuals?</p> <hr /> <div>Should content from the User's and Reference manual be incorporated into this site? Then in the content pages, one could reference a section of Walter's manuals.<br /> --[[User:Saper|Saper]] 22:54, 16 Feb 2005 (CST)</div>

Saper