https://wiki.pymol.org/api.php?action=feedcontributions&user=Oasisbob&feedformat=atomPyMOL Wiki - User contributions [en]2024-03-29T14:09:24ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Select&diff=9699Select2007-05-23T06:26:17Z<p>Oasisbob: added "see also"</p>
<hr />
<div>===DESCRIPTION=== <br />
'''select''' creates a named selection from an atom selection. Selections are one of the most powerful aspects of PyMOL and learning to use selections well is paramount to quickly achieving your goals in PyMOL.<br />
<br />
===USAGE===<br />
select (selection)<br />
select name, (selection)<br />
select name = (selection) # (DEPRECATED)<br />
<br />
===PYMOL API===<br />
<source lang="python"><br />
cmd.select(string name, string selection)<br />
</source><br />
<br />
===EXAMPLES===<br />
select near , (ll expand 8)<br />
select near , (ll expand 8)<br />
select bb, (name ca,n,c,o )<br />
<br />
===NOTES===<br />
Type '''help selections''' for more information about selections. <br />
<br />
===SEE ALSO===<br />
*[[Selection Algebra]]<br />
*[[Property Selectors]]<br />
<br />
[[Category:Commands|select]]</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Settings&diff=10138Settings2007-04-27T18:23:12Z<p>Oasisbob: added link to existing depth_cue page</p>
<hr />
<div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br />
<br />
active_selections ray_default_renderer <br />
[[all_states]] ray_direct_shade <br />
[[ambient]] ray_hint_camera <br />
angle_label_position ray_hint_shadow <br />
angle_size ray_improve_shadows <br />
animation ray_interior_color <br />
animation_duration ray_interior_mode <br />
[[antialias]] ray_interior_reflect <br />
async_builds ray_interior_shadows <br />
[[atom_name_wildcard]] ray_interior_texture <br />
auto_classify_atoms ray_legacy_lighting <br />
auto_color ray_max_passes <br />
auto_dss [[ray_opaque_background]] <br />
auto_hide_selections [[ray_orthoscopic]] <br />
auto_indicate_flags ray_oversample_cutoff <br />
auto_number_selections ray_pixel_scale <br />
auto_remove_hydrogens [[ray_shadow]] <br />
auto_sculpt ray_shadow_decay_factor <br />
auto_show_lines ray_shadow_decay_range <br />
auto_show_nonbonded ray_shadow_fudge <br />
auto_show_selections [[ray_shadows]] <br />
auto_show_spheres ray_texture <br />
[[auto_zoom]] ray_texture_settings <br />
[[backface_cull]] ray_trace_depth_factor <br />
batch_prefix ray_trace_disco_factor <br />
[[bg_rgb]] [[ray_trace_fog]] <br />
bonding_vdw_cutoff ray_trace_fog_start <br />
button_mode [[ray_trace_frames]] <br />
button_mode_name ray_trace_gain <br />
cache_display [[Ray#Modes|ray_trace_mode]]<br />
cache_frames ray_trace_slope_factor <br />
cache_memory ray_transparency_contrast <br />
[[cartoon_color]] ray_transparency_shadows <br />
[[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br />
cartoon_debug ray_transparency_specular <br />
[[cartoon_discrete_colors]] ray_triangle_fudge <br />
[[cartoon_dumbbell_length]] [[reflect]] <br />
[[cartoon_dumbbell_radius]] reflect_power <br />
[[cartoon_dumbbell_width]] retain_order <br />
[[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br />
[[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br />
[[cartoon_flat_cycles]] ribbon_power <br />
[[cartoon_flat_sheets]] ribbon_power_b <br />
[[Cartoon_helix_radius]] ribbon_radius <br />
[[cartoon_highlight_color]] [[ribbon_sampling]] <br />
cartoon_ladder_color ribbon_side_chain_helper <br />
cartoon_ladder_mode [[ribbon_smooth]] <br />
cartoon_ladder_radius ribbon_throw <br />
cartoon_loop_cap ribbon_trace_atoms <br />
cartoon_loop_quality [[ribbon_width]] <br />
cartoon_loop_radius robust_logs <br />
[[cartoon_nucleic_acid_color]] rock_delay <br />
[[cartoon_nucleic_acid_mode]] roving_byres <br />
[[cartoon_oval_length]] roving_cartoon <br />
[[cartoon_oval_quality]] roving_delay <br />
[[cartoon_oval_width]] roving_detail <br />
cartoon_power roving_isomesh <br />
cartoon_power_b roving_isosurface <br />
cartoon_putty_quality roving_labels <br />
cartoon_putty_radius roving_lines <br />
cartoon_putty_range roving_map1_level <br />
cartoon_putty_scale_max roving_map1_name <br />
cartoon_putty_scale_min roving_map2_level <br />
cartoon_putty_scale_power roving_map2_name <br />
[[cartoon_rect_length]] roving_map3_level <br />
[[cartoon_rect_width]] roving_map3_name <br />
cartoon_refine roving_nb_spheres <br />
cartoon_refine_normals roving_nonbonded <br />
cartoon_refine_tips roving_origin <br />
cartoon_ring_color roving_origin_z <br />
cartoon_ring_finder roving_origin_z_cushion <br />
[[cartoon_ring_mode]] roving_polar_contacts <br />
cartoon_ring_radius roving_polar_cutoff <br />
[[cartoon_ring_transparency]] roving_ribbon <br />
cartoon_ring_width roving_selection <br />
[[cartoon_round_helices]] roving_spheres <br />
[[cartoon_sampling]] roving_sticks <br />
[[cartoon_side_chain_helper]] scene_animation <br />
cartoon_smooth_cycles scene_animation_duration <br />
cartoon_smooth_first scene_current_name <br />
cartoon_smooth_last scene_loop <br />
[[cartoon_smooth_loops]] scene_restart_movie_delay <br />
cartoon_throw scenes_changed <br />
cartoon_trace_atoms sculpt_angl_weight <br />
[[cartoon_transparency]] sculpt_auto_center <br />
cartoon_tube_cap sculpt_avd_excl <br />
cartoon_tube_quality sculpt_avd_gap <br />
cartoon_tube_radius sculpt_avd_range <br />
[[cavity_cull]] sculpt_avd_weight <br />
cgo_dot_radius sculpt_bond_weight <br />
cgo_dot_width sculpt_field_mask <br />
cgo_line_radius sculpt_hb_overlap <br />
cgo_line_width sculpt_hb_overlap_base <br />
cgo_ray_width_scale sculpt_line_weight <br />
cgo_sphere_quality sculpt_max_max <br />
cgo_transparency sculpt_max_min <br />
clamp_colors sculpt_max_scale <br />
connect_bonded sculpt_max_weight <br />
connect_cutoff sculpt_memory <br />
connect_mode sculpt_min_max <br />
coulomb_cutoff sculpt_min_min <br />
coulomb_dielectric sculpt_min_scale <br />
coulomb_units_factor sculpt_min_weight <br />
cull_spheres sculpt_nb_interval <br />
[[Dash_Gap]] sculpt_plan_weight <br />
[[Dash_Length]] sculpt_pyra_weight <br />
[[Dash_Radius]] sculpt_tors_tolerance <br />
[[Dash_Round_Ends]] sculpt_tors_weight <br />
dash_width sculpt_tri_max <br />
debug_pick sculpt_tri_min <br />
defer_builds_mode sculpt_tri_mode <br />
defer_updates sculpt_tri_scale <br />
[[depth_cue]] sculpt_tri_weight <br />
dihedral_label_position sculpt_vdw_scale <br />
dihedral_size sculpt_vdw_scale14 <br />
direct sculpt_vdw_vis_max <br />
dist_counter sculpt_vdw_vis_mid <br />
distance_exclusion sculpt_vdw_vis_min <br />
dot_color sculpt_vdw_vis_mode <br />
dot_density sculpt_vdw_weight <br />
dot_hydrogens sculpt_vdw_weight14 <br />
dot_lighting sculpting <br />
dot_mode sculpting_cycles <br />
dot_normals secondary_structure <br />
dot_radius security <br />
dot_solvent sel_counter<br />
[[dot_width]] selection_overlay <br />
draw_frames selection_round_points <br />
editor_auto_dihedral selection_visible_only <br />
editor_auto_origin [[selection_width]] <br />
editor_label_fragments selection_width_max <br />
fast_idle selection_width_scale <br />
fetch_path [[seq_view]] <br />
[[Field_Of_View]] seq_view_alignment <br />
fit_iterations seq_view_color <br />
fit_tolerance seq_view_discrete_by_state <br />
float_labels seq_view_fill_char <br />
[[fog]] seq_view_fill_color <br />
[[fog_start]] seq_view_format <br />
frame seq_view_label_color <br />
full_screen seq_view_label_mode <br />
gamma seq_view_label_spacing <br />
gaussian_b_adjust seq_view_label_start <br />
gaussian_b_floor [[seq_view_location]] <br />
gaussian_resolution seq_view_overlay <br />
gl_ambient seq_view_unaligned_color <br />
h_bond_cone seq_view_unaligned_mode <br />
h_bond_cutoff_center session_file <br />
h_bond_cutoff_edge session_migration <br />
h_bond_exclusion session_version_check <br />
h_bond_max_angle [[shininess]]<br />
h_bond_power_a show_alpha_checker <br />
h_bond_power_b show_progress <br />
[[half_bonds]] simplify_display_lists <br />
hash_max single_image <br />
hide_underscore_names slice_dynamic_grid <br />
idle_delay slice_dynamic_grid_resolution<br />
ignore_case slice_grid <br />
ignore_pdb_segi slice_height_map <br />
image_dots_per_inch slice_height_scale <br />
internal_feedback slice_track_camera <br />
[[Internal Gui|internal_gui]] slow_idle <br />
internal_gui_control_size smooth_color_triangle <br />
internal_gui_mode solvent_radius <br />
internal_gui_width spec_count <br />
[[internal_prompt]] spec_direct <br />
isomesh_auto_state spec_direct_power <br />
[[label_color]] spec_power <br />
[[Label_font_id]] [[spec_reflect]] <br />
[[Label_outline_color]] specular <br />
[[label_position]] specular_intensity <br />
[[label_shadow_mode]] [[sphere_color]] <br />
[[label_size]] sphere_mode <br />
legacy_mouse_zoom sphere_point_max_size <br />
legacy_vdw_radii sphere_point_size <br />
light sphere_quality <br />
light2 [[sphere_scale]] <br />
light3 sphere_solvent <br />
light4 [[sphere_transparency]] <br />
light5 spheroid_fill <br />
light6 spheroid_scale <br />
light7 spheroid_smooth <br />
light8 ss_helix_phi_exclude <br />
light9 ss_helix_phi_include <br />
[[light_count]] ss_helix_phi_target <br />
line_radius ss_helix_psi_exclude <br />
[[line_smooth]] ss_helix_psi_include <br />
line_stick_helper ss_helix_psi_target <br />
line_width ss_strand_phi_exclude <br />
log_box_selections ss_strand_phi_include <br />
log_conformations ss_strand_phi_target <br />
logging ss_strand_psi_exclude <br />
matrix_mode ss_strand_psi_include <br />
max_threads ss_strand_psi_target <br />
max_triangles state <br />
[[mesh_color]] static_singletons <br />
[[mesh_lighting]] stereo <br />
[[mesh_mode]] stereo_angle <br />
mesh_normals stereo_double_pump_mono <br />
[[mesh_quality]] stereo_mode <br />
mesh_radius stereo_shift <br />
mesh_solvent [[stick_ball]] <br />
[[mesh_type]] [[stick_ball_ratio]] <br />
[[mesh_width]] stick_color <br />
[[min_mesh_spacing]] stick_fixed_radius <br />
mouse_limit [[stick_nub]] <br />
mouse_restart_movie_delay stick_overlap <br />
mouse_scale stick_quality <br />
mouse_selection_mode stick_radius <br />
movie_delay [[stick_transparency]] <br />
movie_loop stick_valence_scale <br />
multiplex stop_on_exceptions <br />
no_idle surface_best <br />
nonbonded_size surface_carve_cutoff <br />
normal_workaround surface_carve_selection <br />
normalize_ccp4_maps surface_carve_state <br />
normalize_grd_maps surface_circumscribe <br />
normalize_o_maps surface_clear_cutoff <br />
nvidia_bugs surface_clear_selection <br />
opaque_background surface_clear_state <br />
[[orthoscopic]] surface_color <br />
overlay surface_debug <br />
overlay_lines surface_miserable <br />
pdb_conect_all surface_mode <br />
pdb_discrete_chains surface_normal <br />
pdb_echo_tags surface_optimize_subsets <br />
pdb_hetatm_sort surface_poor <br />
pdb_honor_model_number surface_proximity <br />
pdb_insertions_go_first surface_quality <br />
pdb_insure_orthogonal surface_ramp_above_mode <br />
pdb_literal_names surface_solvent <br />
pdb_no_end_record surface_trim_cutoff <br />
pdb_reformat_names_mode surface_trim_factor <br />
pdb_retain_ids surface_type <br />
pdb_standard_order suspend_updates <br />
pdb_truncate_residue_name swap_dsn6_bytes <br />
pdb_unbond_cations sweep_angle <br />
pdb_use_ter_records sweep_mode <br />
[[pickable]] sweep_phase <br />
png_file_gamma sweep_speed <br />
png_screen_gamma test1 <br />
power test2 <br />
pqr_no_chain_id text <br />
presentation texture_fonts <br />
presentation_auto_quit [[transparency]] <br />
presentation_auto_start transparency_mode <br />
presentation_mode transparency_picking_mode <br />
preserve_chempy_ids triangle_max_passes <br />
pymol_space_max_blue trim_dots <br />
pymol_space_max_green [[two_sided_lighting]]<br />
pymol_space_max_red use_display_lists <br />
pymol_space_min_factor [[valence]] <br />
raise_exceptions valence_default <br />
rank_assisted_sorts valence_size <br />
ray_blend_blue validate_object_names <br />
ray_blend_colors [[virtual_trackball]] <br />
ray_blend_green wildcard <br />
ray_blend_red wizard_prompt_mode <br />
ray_color_ramps wrap_output <br />
<br />
[[Category:Settings|All Settings]]</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8427Practical Pymol for Beginners2007-04-11T16:30:06Z<p>Oasisbob: /* Whoops: Getting unstuck */</p>
<hr />
<div>Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind. <br />
<br />
==The PyMol Interface==<br />
When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) contains the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line.<br />
<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The second window is the PyMOL Viewer, which is where all the magic happens. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. <br />
<br />
The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. PyMOL can display more than one object at a time, and provides an Object Control Panel to adjust viewing modes, colors, labels, hiding, and just about anything else relating to objects. After each object name is a set of command buttons which control the object. Here are the buttons and some of their options:<br />
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations<br />
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view. <br />
* '''H''' - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' is the opposite of '''S''' and hides unwanted representations. <br />
* '''L''' - Label: Label atoms, residues, etc.<br />
* '''C''' - Color: Change the color of atoms and groups. <br />
<br />
The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').<br />
<br />
===About the command line===<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible.<br />
<br />
Although this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative. <br />
<br />
To run any text command, type it in at a '''PyMOL>''' command line and hit ''[Enter]''.<br />
<br />
==Getting started: explore a protein==<br />
PyMol is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.<br />
<br />
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]<br />
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. <br />
# The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons. Each button contains a submenu with more options. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. <br />
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.<br />
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.<br />
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel. <br />
#*Rota: Rotate<br />
#*Move: Translate object along an axis<br />
#*MoveZ: aka Zoom<br />
#*Sele: Select`<br />
#*Slab:<br />
#*Cent:<br />
#*PkAt:<br />
<br />
==What else can this thing do?==<br />
So, now what? Good question. PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy.<br />
<br />
===Saving an image===<br />
You've found the perfect view, and you'd like to save it?<br />
<br />
# Change the size of the viewer and zoom in/out to make the image the right size. Images are saved exactly as they appear in the viewer, and the size of the viewer determines the size of the image.<br />
#* For example, images for printing and presenting should be larger than images for a posting on a website.<br />
# Because PyMOL was designed to run on older computers, the maximum quality is not enabled by default. To change this, select '''Display''', '''Quality''', '''Maximum Quality'''. Notice that round things are rounder, curves are curvier, and color shading is smoother.<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save Image...''' An picture of the current view will be saved in PNG format.<br />
<br />
'''Tip:''' Using the ''[[ray]]'' command before saving an image will create a higher quality version with shadows, etc. This can take time, depending on the size of the image and speed of the computer, but the images created after ray tracing are usually spectacular. However, the ray tracing disappears if the view is changed in any way.<br />
<br />
===Selecting parts of an object===<br />
Sometimes it might be useful to select part of an object and modify it directly; for example, selecting active-site residues in a protein to highlight them in another color. <br />
<br />
In the lower-right corner of the Viewer, next to the animation controls, is an '''S''' button (not to be confused with the '''S'''how button in the object control panel) that activates the selection tool. The selection tool can be changed to select atoms or residues by clicking ''Selecting Residues(or whatever)'' until the right mode appears.<br />
<br />
Once selecting is activated, a list of parts to select appears at the top of the Viewer. Select things clicking or dragging across a range.<br />
<br />
Selections can be controlled individually in the object control panel, just like any other object. To save a selection, select '''rename''' from the '''A''' menu.<br />
<br />
===Whoops: Getting unstuck===<br />
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common problems:<br />
<br />
* ''The model disappeared:'' Sometimes while rotating and moving a model, it can get lost. Right-click the background of the viewer, and select '''reset''' from the ''Main Pop-Up''. The model should return to view; if it doesn't, make sure the object is being drawn using the '''S''' menu.<br />
* ''The model has funny colors, labels, etc and they won't go away:'' The '''H''' menu in the object control panel will remove unwanted details; however, sometimes it's difficult to know exactly what to remove. Select '''H''', then '''everything''' to hide all details and start fresh.<br />
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state, but all work will be lost.<br />
<br />
==Coming Soon==<br />
===Saving work===<br />
===Scripting===<br />
===Logging===</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8426Practical Pymol for Beginners2007-04-11T04:42:49Z<p>Oasisbob: /* Whoops: Getting unstuck */</p>
<hr />
<div>Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind. <br />
<br />
==The PyMol Interface==<br />
When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) contains the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line.<br />
<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The second window is the PyMOL Viewer, which is where all the magic happens. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. <br />
<br />
The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. PyMOL can display more than one object at a time, and provides an Object Control Panel to adjust viewing modes, colors, labels, hiding, and just about anything else relating to objects. After each object name is a set of command buttons which control the object. Here are the buttons and some of their options:<br />
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations<br />
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view. <br />
* '''H''' - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' is the opposite of '''S''' and hides unwanted representations. <br />
* '''L''' - Label: Label atoms, residues, etc.<br />
* '''C''' - Color: Change the color of atoms and groups. <br />
<br />
The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').<br />
<br />
===About the command line===<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible.<br />
<br />
Although this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative. <br />
<br />
To run any text command, type it in at a '''PyMOL>''' command line and hit ''[Enter]''.<br />
<br />
==Getting started: explore a protein==<br />
PyMol is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.<br />
<br />
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]<br />
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. <br />
# The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons. Each button contains a submenu with more options. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. <br />
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.<br />
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.<br />
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel. <br />
#*Rota: Rotate<br />
#*Move: Translate object along an axis<br />
#*MoveZ: aka Zoom<br />
#*Sele: Select`<br />
#*Slab:<br />
#*Cent:<br />
#*PkAt:<br />
<br />
==What else can this thing do?==<br />
So, now what? Good question. PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy.<br />
<br />
===Saving an image===<br />
You've found the perfect view, and you'd like to save it?<br />
<br />
# Change the size of the viewer and zoom in/out to make the image the right size. Images are saved exactly as they appear in the viewer, and the size of the viewer determines the size of the image.<br />
#* For example, images for printing and presenting should be larger than images for a posting on a website.<br />
# Because PyMOL was designed to run on older computers, the maximum quality is not enabled by default. To change this, select '''Display''', '''Quality''', '''Maximum Quality'''. Notice that round things are rounder, curves are curvier, and color shading is smoother.<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save Image...''' An picture of the current view will be saved in PNG format.<br />
<br />
'''Tip:''' Using the ''[[ray]]'' command before saving an image will create a higher quality version with shadows, etc. This can take time, depending on the size of the image and speed of the computer, but the images created after ray tracing are usually spectacular. However, the ray tracing disappears if the view is changed in any way.<br />
<br />
===Selecting parts of an object===<br />
Sometimes it might be useful to select part of an object and modify it directly; for example, selecting active-site residues in a protein to highlight them in another color. <br />
<br />
In the lower-right corner of the Viewer, next to the animation controls, is an '''S''' button (not to be confused with the '''S'''how button in the object control panel) that activates the selection tool. The selection tool can be changed to select atoms or residues by clicking ''Selecting Residues(or whatever)'' until the right mode appears.<br />
<br />
Once selecting is activated, a list of parts to select appears at the top of the Viewer. Select things clicking or dragging across a range.<br />
<br />
Selections can be controlled individually in the object control panel, just like any other object. To save a selection, select '''rename''' from the '''A''' menu.<br />
<br />
===Whoops: Getting unstuck===<br />
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:<br />
<br />
* ''The model disappeared:'' Sometimes while rotating and moving a model, it can get lost. Right-click the background of the viewer, and select '''reset''' from the ''Main Pop-Up''. The model should return to view; if it doesn't, make sure the object is being drawn using the '''S''' menu.<br />
* ''The model has funny colors, labels, etc and they won't go away:'' The '''H''' menu in the object control panel will remove unwanted details; however, sometimes it's difficult to know exactly what to remove. Select '''H''', then '''everything''' to hide all details and start fresh.<br />
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.<br />
<br />
==Coming Soon==<br />
===Saving work===<br />
===Scripting===<br />
===Logging===</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8425Practical Pymol for Beginners2007-04-11T04:31:47Z<p>Oasisbob: /* Saving an image */</p>
<hr />
<div>Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind. <br />
<br />
==The PyMol Interface==<br />
When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) contains the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line.<br />
<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The second window is the PyMOL Viewer, which is where all the magic happens. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. <br />
<br />
The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. PyMOL can display more than one object at a time, and provides an Object Control Panel to adjust viewing modes, colors, labels, hiding, and just about anything else relating to objects. After each object name is a set of command buttons which control the object. Here are the buttons and some of their options:<br />
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations<br />
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view. <br />
* '''H''' - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' is the opposite of '''S''' and hides unwanted representations. <br />
* '''L''' - Label: Label atoms, residues, etc.<br />
* '''C''' - Color: Change the color of atoms and groups. <br />
<br />
The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').<br />
<br />
===About the command line===<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible.<br />
<br />
Although this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative. <br />
<br />
To run any text command, type it in at a '''PyMOL>''' command line and hit ''[Enter]''.<br />
<br />
==Getting started: explore a protein==<br />
PyMol is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.<br />
<br />
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]<br />
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. <br />
# The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons. Each button contains a submenu with more options. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. <br />
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.<br />
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.<br />
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel. <br />
#*Rota: Rotate<br />
#*Move: Translate object along an axis<br />
#*MoveZ: aka Zoom<br />
#*Sele: Select`<br />
#*Slab:<br />
#*Cent:<br />
#*PkAt:<br />
<br />
==What else can this thing do?==<br />
So, now what? Good question. PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy.<br />
<br />
===Saving an image===<br />
You've found the perfect view, and you'd like to save it?<br />
<br />
# Change the size of the viewer and zoom in/out to make the image the right size. Images are saved exactly as they appear in the viewer, and the size of the viewer determines the size of the image.<br />
#* For example, images for printing and presenting should be larger than images for a posting on a website.<br />
# Because PyMOL was designed to run on older computers, the maximum quality is not enabled by default. To change this, select '''Display''', '''Quality''', '''Maximum Quality'''. Notice that round things are rounder, curves are curvier, and color shading is smoother.<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save Image...''' An picture of the current view will be saved in PNG format.<br />
<br />
'''Tip:''' Using the ''[[ray]]'' command before saving an image will create a higher quality version with shadows, etc. This can take time, depending on the size of the image and speed of the computer, but the images created after ray tracing are usually spectacular. However, the ray tracing disappears if the view is changed in any way.<br />
<br />
===Selecting parts of an object===<br />
Sometimes it might be useful to select part of an object and modify it directly; for example, selecting active-site residues in a protein to highlight them in another color. <br />
<br />
In the lower-right corner of the Viewer, next to the animation controls, is an '''S''' button (not to be confused with the '''S'''how button in the object control panel) that activates the selection tool. The selection tool can be changed to select atoms or residues by clicking ''Selecting Residues(or whatever)'' until the right mode appears.<br />
<br />
Once selecting is activated, a list of parts to select appears at the top of the Viewer. Select things clicking or dragging across a range.<br />
<br />
Selections can be controlled individually in the object control panel, just like any other object. To save a selection, select '''rename''' from the '''A''' menu.<br />
<br />
===Whoops: Getting unstuck===<br />
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:<br />
<br />
* ''The model disappeared:'' Sometimes while rotating and moving a model, it can get lost. Right-click the background of the viewer, and select '''reset''' from the ''Main Pop-Up''. The model should return to view; if it doesn't, make sure the object is being drawn using the '''S''' menu.<br />
* ''The model has funny colors, labels, etc and they won't go away:'' The '''H''' menu in the object control panel will remove unwanted details; however, sometimes it's difficult to know exactly what to remove. Select '''H''', then '''everything''' to hide all details. <br />
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.<br />
<br />
==Coming Soon==<br />
===Saving work===<br />
===Scripting===<br />
===Logging===</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8424Practical Pymol for Beginners2007-04-11T04:25:37Z<p>Oasisbob: </p>
<hr />
<div>Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind. <br />
<br />
==The PyMol Interface==<br />
When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) contains the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line.<br />
<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The second window is the PyMOL Viewer, which is where all the magic happens. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. <br />
<br />
The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. PyMOL can display more than one object at a time, and provides an Object Control Panel to adjust viewing modes, colors, labels, hiding, and just about anything else relating to objects. After each object name is a set of command buttons which control the object. Here are the buttons and some of their options:<br />
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations<br />
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view. <br />
* '''H''' - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' is the opposite of '''S''' and hides unwanted representations. <br />
* '''L''' - Label: Label atoms, residues, etc.<br />
* '''C''' - Color: Change the color of atoms and groups. <br />
<br />
The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').<br />
<br />
===About the command line===<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible.<br />
<br />
Although this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative. <br />
<br />
To run any text command, type it in at a '''PyMOL>''' command line and hit ''[Enter]''.<br />
<br />
==Getting started: explore a protein==<br />
PyMol is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.<br />
<br />
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]<br />
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. <br />
# The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons. Each button contains a submenu with more options. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. <br />
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.<br />
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.<br />
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel. <br />
#*Rota: Rotate<br />
#*Move: Translate object along an axis<br />
#*MoveZ: aka Zoom<br />
#*Sele: Select`<br />
#*Slab:<br />
#*Cent:<br />
#*PkAt:<br />
<br />
==What else can this thing do?==<br />
So, now what? Good question. PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy.<br />
<br />
===Saving an image===<br />
You've found the perfect view, and you'd like to save it?<br />
<br />
# Change the size of the viewer and zoom in/out to make the image the right size. Images are saved exactly as they appear in the viewer, including size.<br />
#* For example, images for printing and presenting should be larger than images for a posting on a website.<br />
# Because PyMOL was designed to run on older computers, the maximum quality is not enabled by default. To change this, select '''Display''', '''Quality''', '''Maximum Quality'''. Notice that round things are rounder, curves are curvier, and color shading is smoother.<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save Image...''' An picture of the current view will be saved in PNG format.<br />
<br />
'''Tip:''' Using the ''[[ray]]'' command before saving an image will create a higher quality version with shadows, etc. This can take time, depending on the size of the image and speed of the computer, but the images created after ray tracing are usually spectacular. However, the ray tracing disappears if the view is changed in any way.<br />
<br />
===Selecting parts of an object===<br />
Sometimes it might be useful to select part of an object and modify it directly; for example, selecting active-site residues in a protein to highlight them in another color. <br />
<br />
In the lower-right corner of the Viewer, next to the animation controls, is an '''S''' button (not to be confused with the '''S'''how button in the object control panel) that activates the selection tool. The selection tool can be changed to select atoms or residues by clicking ''Selecting Residues(or whatever)'' until the right mode appears.<br />
<br />
Once selecting is activated, a list of parts to select appears at the top of the Viewer. Select things clicking or dragging across a range.<br />
<br />
Selections can be controlled individually in the object control panel, just like any other object. To save a selection, select '''rename''' from the '''A''' menu.<br />
<br />
===Whoops: Getting unstuck===<br />
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:<br />
<br />
* ''The model disappeared:'' Sometimes while rotating and moving a model, it can get lost. Right-click the background of the viewer, and select '''reset''' from the ''Main Pop-Up''. The model should return to view; if it doesn't, make sure the object is being drawn using the '''S''' menu.<br />
* ''The model has funny colors, labels, etc and they won't go away:'' The '''H''' menu in the object control panel will remove unwanted details; however, sometimes it's difficult to know exactly what to remove. Select '''H''', then '''everything''' to hide all details. <br />
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.<br />
<br />
==Coming Soon==<br />
===Saving work===<br />
===Scripting===<br />
===Logging===</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Talk:Practical_Pymol_for_Beginners&diff=10668Talk:Practical Pymol for Beginners2007-04-11T03:48:15Z<p>Oasisbob: New page: This page is still in a work in progress. ~~~~ ==TODO:== * Capitalization for internal GUI features? * Definition of an object? * Objects vs selection objects? * Pic of External GUI for c...</p>
<hr />
<div>This page is still in a work in progress. [[User:Oasisbob|Oasisbob]] 22:48, 10 April 2007 (CDT)<br />
<br />
==TODO:==<br />
* Capitalization for internal GUI features?<br />
* Definition of an object?<br />
* Objects vs selection objects?<br />
* Pic of External GUI for command line<br />
* s/PyMol/PyMOL<br />
* Dummy-style advanced notation.<br />
* Howto run commands...<br />
** Tone change.<br />
* intro and outro</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8423Practical Pymol for Beginners2007-04-11T03:47:27Z<p>Oasisbob: </p>
<hr />
<div>Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind. <br />
<br />
==The PyMol Interface==<br />
When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) has the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), a set of buttons which are shortcuts to common commands, and the command line.<br />
<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The second window is the PyMOL Viewer, which is where all the magic happens. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. <br />
<br />
<br />
The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. PyMOL can display more than one object at a time, and provides an Object Control Panel to adjust viewing modes, colors, labels, hiding, and just about anything else relating to objects. After each object name is a set of command buttons which control the object. Here are the buttons and some of their options:<br />
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations<br />
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view. <br />
* '''H''' - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' is the opposite of '''S''' and hides unwanted representations. <br />
* '''L''' - Label: Label atoms, residues, etc.<br />
* '''C''' - Color: Change the color of atoms and groups. <br />
<br />
The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').<br />
<br />
===About the command line===<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative. To run any text command, type it in at a '''PyMOL>''' command line and hit ''[Enter]''.<br />
<br />
==Getting started: explore a protein==<br />
PyMol is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.<br />
<br />
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]<br />
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. <br />
# The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons. Each button contains a submenu with more options. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. <br />
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.<br />
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.<br />
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel. <br />
#*Rota: Rotate<br />
#*Move: Translate object along an axis<br />
#*MoveZ: aka Zoom<br />
<br />
<br />
==What else is this thing good for?==<br />
So, now what? Good question. PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy.<br />
<br />
===Saving an image===<br />
You've found the perfect view, and you'd like to save it?<br />
<br />
# Change the size of the viewer and zoom in/out to make the image the right size. Images are saved exactly as they appear in the viewer, including size.<br />
#* For example, images for printing and presenting should be larger than images for a posting on a website.<br />
# Because PyMOL was designed to run on older computers, the maximum quality is not enabled by default. To change this, select '''Display''', '''Quality''', '''Maximum Quality'''. Notice that round things are rounder, curves are curvier, and color shading is smoother.<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save Image...''' An picture of the current view will be saved in PNG format.<br />
<br />
'''Tip:''' Using the ''[[ray]]'' command before saving an image will create a higher quality version of the molecule with shadows, etc. Depending on the size of the image and speed of the computer, it can take a while (seconds to minutes...), but the images created with ray tracing are usually spectacular. However, the ray tracing disappears if the view is changed in any way.<br />
<br />
===Whoops: Getting unstuck===<br />
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:<br />
<br />
* ''The model disappeared:'' Sometimes while rotating and moving a model, it can get lost. Right-click the background of the viewer, and select '''reset''' from the ''Main Pop-Up''. The model should return to view; if it doesn't, make sure the object is being drawn using the '''S''' menu.<br />
* ''The model has funny colors, labels, etc and they won't go away:'' The '''H''' menu in the object control panel will remove unwanted details; however, sometimes it's difficult to know exactly what to remove. Select '''H''', then '''everything''' to hide all details. <br />
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8422Practical Pymol for Beginners2007-04-11T03:29:56Z<p>Oasisbob: more changes</p>
<hr />
<div>Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind. <br />
<br />
==The PyMol Interface==<br />
When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) has the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), a set of buttons which are shortcuts to common commands, and the command line.<br />
<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The second window is the PyMOL Viewer, which is where all the magic happens. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. <br />
<br />
<br />
The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. PyMOL can display more than one object at a time, and provides an Object Control Panel to adjust viewing modes, colors, labels, hiding, and just about anything else relating to objects. After each object name is a set of command buttons which control the object. Here are the buttons and some of their options:<br />
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations<br />
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view. <br />
* '''H''' - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' is the opposite of '''S''' and hides unwanted representations. <br />
* '''L''' - Label: Label atoms, residues, etc.<br />
* '''C''' - Color: Change the color of atoms and groups. <br />
<br />
The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').<br />
<br />
===About the command line===<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative. To run any text command, type it in at a '''PyMOL>''' command line and hit ''[Enter]''.<br />
<br />
==Getting started: explore a protein==<br />
PyMol is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.<br />
<br />
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. <br />
# The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons. Each button contains a submenu with more options. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. <br />
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.<br />
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.<br />
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]<br />
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel. <br />
#*Rota: Rotate<br />
#*Move: Translate object along an axis<br />
#*MoveZ: aka Zoom<br />
<br />
<br />
So, now what? Good question. PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy.<br />
<br />
==Saving an image==<br />
You've found the perfect view, and you'd like to save it?<br />
<br />
# Images are saved exactly as they appear in the viewer, including size. Change the window size and zoom in/out if it's not the proper size.<br />
#* For example, images for printing and presenting should be larger than images for a posting on a website.<br />
# Because PyMOL was designed to run on older computers, the maximum quality is not enabled by default. To change this, select '''Display''', '''Quality''', '''Maximum Quality'''. Notice that round things are rounder, curves are curvier, and color shading is smoother.<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save Image...''' An picture of the current view will be saved in PNG format.<br />
<br />
'''Advanced:''' Using the ''[[ray]]'' command before saving will create a higher quality version of the molecule with shadows, etc. Depending on the size of the image and speed of the computer, it can take a while (seconds to minutes...), but the images created with ray tracing are usually spectacular. However, the ray tracing disappears if the view is changed in any way.<br />
<br />
==Getting unstuck==<br />
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:<br />
<br />
* ''The model disappeared:'' Sometimes while rotating and moving a model, it can get lost. Right-click the background of the viewer, and the ''Main Pop-Up'' should appear. Select '''reset''', and the model should return to view.<br />
* ''The model has funny colors, labels, etc and they won't go away:'' The '''H''' menu in the object control panel will remove unwanted details; however, sometimes it's difficult to know exactly what to remove. Select '''H''', then '''everything''' to hide all details. <br />
<br />
==Other==<br />
* Reinitialize hint<br />
<br />
<br />
==TODO:==<br />
* Capitalization for internal GUI features?<br />
* Definition of an object?<br />
* Objects vs selection objects?<br />
* Pic of External GUI for command line<br />
* s/PyMol/PyMOL<br />
* Dummy-style advanced notation.<br />
* Howto run commands...<br />
** Tone change.<br />
* intro and outro</div>Oasisbobhttps://wiki.pymol.org/index.php?title=File:Mouse-3view.png&diff=2154File:Mouse-3view.png2007-04-11T02:09:20Z<p>Oasisbob: Mouse button assignments for default 3-button viewing mode</p>
<hr />
<div>Mouse button assignments for default 3-button viewing mode</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8421Practical Pymol for Beginners2007-04-10T21:55:57Z<p>Oasisbob: more text</p>
<hr />
<div>Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind. <br />
<br />
==The PyMol Interface==<br />
When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) has the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), a set of buttons which are shortcuts to common commands, and the command line.<br />
<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The second window is the PyMol viewer, which is where all the magic happens. In the viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. The Object Control Panel is used to change colors, viewing mode, apply labels, remove objects, and just about anything else relating to objects. (An object is normally a group of molecules loaded from a PDB coordinate file.) Each object is displayed by name followed by a set of command buttons which control the object. Here are the menus and some of their options:<br />
* A - Actions: Close, etc<br />
* S - Show: Change the way an object is represented, eg change stick view to cartoon view. <br />
* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations. <br />
* L - Label: Label atoms, residues, etc.<br />
* C - Color: Change the color of atoms and groups. <br />
<br />
The lower-left corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').<br />
<br />
==About the command line==<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.<br />
<br />
==Visualize a protein==<br />
These instructions cover opening a PDB file and using PyMol as tool for molecular exploration.<br />
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. <br />
# The right side of the Viewer shows objects loaded from the PDB, and the command buttons. Each button contains a submenu that can be used to manipulate the object. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. <br />
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.<br />
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.<br />
# Click and drag the protein to change the view. Reminder: a legend for mouse actions is below the object control panel. <br />
#*(Cover mouse matrix abbreviations)<br />
<br />
So, now what? Good question. PyMOL is a powerful program, and everyone uses it for something different. The remainder of this guide is devoted to common tasks that come in handy.<br />
<br />
==Saving an image==<br />
You've found the perfect view, and you'd like to save it?<br />
<br />
# Images are saved exactly as they appear in the viewer, including size. Change the window size and zoom in/out if it's not the proper size.<br />
#* For example, images for printing and presenting should be larger than images for a posting on a website.<br />
# Because PyMOL was designed to run on older computers, the maximum quality is not enabled by default. To change this, select '''Display''', '''Quality''', '''Maximum Quality'''. Notice that round things are rounder, curves are curvier, and color shading is smoother.<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save Image...''' An picture of the current view will be saved in PNG format.<br />
<br />
'''Advanced:''' Using the ''[[ray]]'' command before saving will create a higher quality version of the molecule with shadows, etc. Depending on the size of the image and speed of the computer, it can take a while (seconds to minutes...), but the images created with ray tracing are usually spectacular. However, the ray tracing disappears if the view is changed in any way.<br />
<br />
==Getting unstuck==<br />
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:<br />
<br />
* ''The model disappeared:'' Sometimes while rotating and moving a model, it can get lost. Right-click the background of the viewer, and the ''Main Pop-Up'' should appear. Select '''reset''', and the model should return to view.<br />
* ''The model has funny colors, labels, etc and they won't go away:'' The '''H''' menu in the object control panel will remove unwanted details; however, sometimes it's difficult to know exactly what to remove. Select '''H''', then '''everything''' to hide all details. <br />
<br />
==Other==<br />
* Reinitialize hint<br />
<br />
<br />
==TODO:==<br />
* Capitalization for internal GUI features?<br />
* Definition of an object?<br />
* Objects vs selection objects?<br />
* Pic of External GUI for command line<br />
* s/PyMol/PyMOL<br />
* Dummy-style advanced notation.<br />
* Howto run commands...<br />
** Tone change.<br />
* intro and outro</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8420Practical Pymol for Beginners2007-04-10T20:47:42Z<p>Oasisbob: added some images, still a work in progress...</p>
<hr />
<div>Although PyMol has a powerful and flexible command line interface, it can appear daunting to new users. This guide is intended to introduce PyMol basics without leaving the mouse behind. <br />
<br />
==About the command line==<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate changes. Page upon page of PyMol documentation cover these commands, so we're going to ignore them.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative, not required.<br />
<br />
==About the viewer==<br />
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]<br />
The PyMol Viewer is where the 3D models are displayed, and allows the user to interact with the models. The Object Control Panel is used to change colors, viewing mode, apply labels, remove objects, and just about anything else relating to objects. (An object is normally a group of molecules loaded from a PDB coordinate file.) Each object is displayed by name followed by a set of command buttons which change or manipulate the object. Here are the menus and some of their options:<br />
* A - Actions: Close, etc<br />
* S - Show: Change the way an object is represented, eg change stick view to cartoon view. <br />
* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations. <br />
* L - Label: Label atoms, residues, etc.<br />
* C - Color: Change the color of atoms and groups. <br />
<br />
==Visualize a protein==<br />
These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this: <br />
[[Image:Kchannel-rainbow.png|thumb|center|click to see full image]]<br />
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/|RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.)<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks. <br />
# On the left side of the PyMol window is the objects loaded from the PDB, and the command buttons. Each button contains a submenu that can be used to manipulate the object. Click '''S''', then '''cartoon''' to show the protein's secondary structure in typical cartoon form. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''Chainbows''' from the '''By Chain''' menu. <br />
# Click and drag the protein to change the view. A legend for mouse actions is below the object control panel. <br />
#*(Cover mouse matrix abbreviations)<br />
<br />
<br />
<br />
==Save an image==<br />
# Once you've found the appropriate view, save an image using '''File''', '''Save image...''' An picture of the current view will be saved in PNG format.<br />
#* Using the ''ray'' command before saving will draw a higher quality version of the molecule with shadows, etc.<br />
<br />
<br />
<br />
==Other==<br />
* Reinitialize hint<br />
<br />
<br />
==TODO:==<br />
* Capitalization for internal GUI features?<br />
* Definition of an object?<br />
* Objects vs selection objects?<br />
* Pic of External GUI for command line</div>Oasisbobhttps://wiki.pymol.org/index.php?title=File:Viewer_guide.png&diff=2895File:Viewer guide.png2007-04-10T20:34:27Z<p>Oasisbob: A labeled legend of the PyMol interface.</p>
<hr />
<div>A labeled legend of the PyMol interface.</div>Oasisbobhttps://wiki.pymol.org/index.php?title=File:Kchannel-rainbow.png&diff=2117File:Kchannel-rainbow.png2007-04-10T20:03:38Z<p>Oasisbob: An example rendering of the K+ Channel from PDB 1BL8</p>
<hr />
<div>An example rendering of the K+ Channel from PDB 1BL8</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8419Practical Pymol for Beginners2007-04-10T03:32:24Z<p>Oasisbob: /* Visualize a protein */</p>
<hr />
<div>Although PyMol has a powerful and flexible command line interface, it can appear daunting to new users. This guide is intended to introduce PyMol basics without leaving the mouse behind. <br />
<br />
==About the command line==<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate changes. Page upon page of PyMol documentation cover these commands, so we're going to ignore them.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.<br />
<br />
==Visualize a protein==<br />
These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this: <br />
# Obtain a PDB file of your favorite protein. (The [http://www.pdb.org/|RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.)<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks. <br />
# On the left side of the PyMol window is the objects loaded from the PDB, and the command buttons. Each button contains a submenu that can be used to manipulate the object. Click '''S''', then '''cartoon''' to show the protein's secondary structure in typical cartoon form. Here are the menus and some of their options:<br />
#* A - Actions: Close, etc<br />
#* S - Show: Change the way an object is represented, eg change stick view to cartoon view. <br />
#* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations. <br />
#* L - Label: Label atoms, residues, etc.<br />
#* C - Color: Change the color of atoms and groups. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''Chainbows''' from the '''By Chain''' menu. <br />
# Click and drag the protein to change the view. A legend for mouse actions is below the command buttons. <br />
# Once you've found the appropriate view, save an image using '''File''', '''Save image...''' An picture of the current view will be saved in PNG format.<br />
#* Using the ''ray'' command before saving will draw a higher quality version of the molecule with shadows, etc.<br />
<br />
==Other==<br />
* Reinitialize hint</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8418Practical Pymol for Beginners2007-04-10T03:30:06Z<p>Oasisbob: </p>
<hr />
<div>Although PyMol has a powerful and flexible command line interface, it can appear daunting to new users. This guide is intended to introduce PyMol basics without leaving the mouse behind. <br />
<br />
==About the command line==<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate changes. Page upon page of PyMol documentation cover these commands, so we're going to ignore them.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.<br />
<br />
==Visualize a protein==<br />
These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this: <br />
# Obtain a PDB file of your favorite protein. (The [http://www.pdb.org/|RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.)<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks. <br />
# On the left side of the PyMol window is the objects loaded from the PDB, and the command buttons. Each button contains a submenu that can be used to manipulate the object. Click '''S''', then '''cartoon''' to show the protein's secondary structure in typical cartoon form. Here are the menus and some of their options:<br />
#* A - Actions: Close, etc<br />
#* S - Show: Change the way an object is represented, eg change stick view to cartoon view. <br />
#* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations. <br />
#* L - Label: Label atoms, residues, etc.<br />
#* C - Color: Change the color of atoms and groups. <br />
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''Chainbows''' from the '''By Chain''' menu. <br />
# Click and drag the protein to change the view. A legend for mouse actions is below the command buttons. <br />
# Once you've found the appropriate view, save an image using '''File''', '''Save image...''' An picture of the current view will be saved in PNG format.<br />
#* <br />
<br />
==Other==<br />
* Reinitialize hint</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8417Practical Pymol for Beginners2007-04-10T03:04:52Z<p>Oasisbob: /* Visualize a protein */</p>
<hr />
<div>Although PyMol has a powerful and flexible command line interface, it can appear daunting to new users. This guide is intended to introduce PyMol basics without leaving the mouse behind. <br />
<br />
==About the command line==<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate changes. Page upon page of PyMol documentation cover these commands, so we're going to ignore them.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.<br />
<br />
==Visualize a protein==<br />
These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this: <br />
# Obtain a PDB file of your favorite protein. (The [http://www.pdb.org/|RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.)<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks. <br />
# On the left side of the PyMol window is the <br />
<br />
sdf<br />
<br />
==Saving an image==<br />
<br />
<br />
==Other==<br />
* Reinitialize hint</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Practical_Pymol_for_Beginners&diff=8416Practical Pymol for Beginners2007-04-10T02:49:59Z<p>Oasisbob: New page: Although PyMol has a powerful and flexible command line interface, it can appear daunting to new users. This guide is intended to introduce PyMol basics without leaving the mouse behind. ...</p>
<hr />
<div>Although PyMol has a powerful and flexible command line interface, it can appear daunting to new users. This guide is intended to introduce PyMol basics without leaving the mouse behind. <br />
<br />
==About the command line==<br />
The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate changes. Page upon page of PyMol documentation cover these commands, so we're going to ignore them.<br />
<br />
Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.<br />
<br />
==Visualize a protein==<br />
# Obtain a PDB file of your favorite protein. (The [http://www.pdb.org/|RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.)<br />
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks. <br />
# <br />
<br />
sdf<br />
==Saving an image==<br />
<br />
<br />
==Other==<br />
* Reinitialize hint</div>Oasisbobhttps://wiki.pymol.org/index.php?title=Category:Uncategorized&diff=3963Category:Uncategorized2007-04-10T02:05:27Z<p>Oasisbob: beginning pymol beginners tutorial</p>
<hr />
<div>==Alter key bindings==<br />
It's not GUI, but you could simply bind a function key such as F1 to a command:<br />
<source lang="python"><br />
cmd.set_key('F1',lambda :cmd.show('sticks'))<br />
</source><br />
<br />
==Coloring Surface with Electrostatic Potential==<br />
You have to load the potential data by Delphi or some other program like AMBER version 9:<br />
<source lang="python"><br />
load sample.pdb, molecule<br />
load sample.delphi, potential<br />
show surface, molecule<br />
ramp_new level, potential, [-7,0,7]<br />
set surface_color, level, molecule<br />
</source><br />
<br />
==Van der Waals radii==<br />
van der Waals Radii are hard coded in Pymol.<br />
They may be obtained for given atoms from:<br />
<source lang="python"><br />
iterate (name C), print vdw<br />
</source><br />
Default values are:<br />
*C : 1.70<br />
*O : 1.52<br />
*N : 1.55<br />
*H : 1.20<br />
*P : 1.80<br />
<br />
and may be changed with the command [[alter]]<br />
<br />
==Tutorial for Beginners==<br />
I'm in the process of writing a PyMol tutorial for first time users. Intended for undergraduate biology/biochemistry students with no previous visualization experience, it will focus on common operations and practical uses. For now, I'm calling it [[Practical Pymol for Beginners]]. I'm not sure where to categorize it.</div>Oasisbob