PyMOL Wiki - User contributions [en]

Select

2007-05-23T06:26:17Z

Oasisbob: added "see also"

===DESCRIPTION===
'''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.

===USAGE===
select (selection)
select name, (selection)
select name = (selection) # (DEPRECATED)

===PYMOL API===
<source lang="python">
cmd.select(string name, string selection)
</source>

===EXAMPLES===
select near , (ll expand 8)
select near , (ll expand 8)
select bb, (name ca,n,c,o )

===NOTES===
Type '''help selections''' for more information about selections.

===SEE ALSO===
*[[Selection Algebra]]
*[[Property Selectors]]

[[Category:Commands|select]]

Settings

2007-04-27T18:23:12Z

Oasisbob: added link to existing depth_cue page

These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !

active_selections ray_default_renderer
[[all_states]] ray_direct_shade
[[ambient]] ray_hint_camera
angle_label_position ray_hint_shadow
angle_size ray_improve_shadows
animation ray_interior_color
animation_duration ray_interior_mode
[[antialias]] ray_interior_reflect
async_builds ray_interior_shadows
[[atom_name_wildcard]] ray_interior_texture
auto_classify_atoms ray_legacy_lighting
auto_color ray_max_passes
auto_dss [[ray_opaque_background]]
auto_hide_selections [[ray_orthoscopic]]
auto_indicate_flags ray_oversample_cutoff
auto_number_selections ray_pixel_scale
auto_remove_hydrogens [[ray_shadow]]
auto_sculpt ray_shadow_decay_factor
auto_show_lines ray_shadow_decay_range
auto_show_nonbonded ray_shadow_fudge
auto_show_selections [[ray_shadows]]
auto_show_spheres ray_texture
[[auto_zoom]] ray_texture_settings
[[backface_cull]] ray_trace_depth_factor
batch_prefix ray_trace_disco_factor
[[bg_rgb]] [[ray_trace_fog]]
bonding_vdw_cutoff ray_trace_fog_start
button_mode [[ray_trace_frames]]
button_mode_name ray_trace_gain
cache_display [[Ray#Modes|ray_trace_mode]]
cache_frames ray_trace_slope_factor
cache_memory ray_transparency_contrast
[[cartoon_color]] ray_transparency_shadows
[[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut
cartoon_debug ray_transparency_specular
[[cartoon_discrete_colors]] ray_triangle_fudge
[[cartoon_dumbbell_length]] [[reflect]]
[[cartoon_dumbbell_radius]] reflect_power
[[cartoon_dumbbell_width]] retain_order
[[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]]
[[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode
[[cartoon_flat_cycles]] ribbon_power
[[cartoon_flat_sheets]] ribbon_power_b
[[Cartoon_helix_radius]] ribbon_radius
[[cartoon_highlight_color]] [[ribbon_sampling]]
cartoon_ladder_color ribbon_side_chain_helper
cartoon_ladder_mode [[ribbon_smooth]]
cartoon_ladder_radius ribbon_throw
cartoon_loop_cap ribbon_trace_atoms
cartoon_loop_quality [[ribbon_width]]
cartoon_loop_radius robust_logs
[[cartoon_nucleic_acid_color]] rock_delay
[[cartoon_nucleic_acid_mode]] roving_byres
[[cartoon_oval_length]] roving_cartoon
[[cartoon_oval_quality]] roving_delay
[[cartoon_oval_width]] roving_detail
cartoon_power roving_isomesh
cartoon_power_b roving_isosurface
cartoon_putty_quality roving_labels
cartoon_putty_radius roving_lines
cartoon_putty_range roving_map1_level
cartoon_putty_scale_max roving_map1_name
cartoon_putty_scale_min roving_map2_level
cartoon_putty_scale_power roving_map2_name
[[cartoon_rect_length]] roving_map3_level
[[cartoon_rect_width]] roving_map3_name
cartoon_refine roving_nb_spheres
cartoon_refine_normals roving_nonbonded
cartoon_refine_tips roving_origin
cartoon_ring_color roving_origin_z
cartoon_ring_finder roving_origin_z_cushion
[[cartoon_ring_mode]] roving_polar_contacts
cartoon_ring_radius roving_polar_cutoff
[[cartoon_ring_transparency]] roving_ribbon
cartoon_ring_width roving_selection
[[cartoon_round_helices]] roving_spheres
[[cartoon_sampling]] roving_sticks
[[cartoon_side_chain_helper]] scene_animation
cartoon_smooth_cycles scene_animation_duration
cartoon_smooth_first scene_current_name
cartoon_smooth_last scene_loop
[[cartoon_smooth_loops]] scene_restart_movie_delay
cartoon_throw scenes_changed
cartoon_trace_atoms sculpt_angl_weight
[[cartoon_transparency]] sculpt_auto_center
cartoon_tube_cap sculpt_avd_excl
cartoon_tube_quality sculpt_avd_gap
cartoon_tube_radius sculpt_avd_range
[[cavity_cull]] sculpt_avd_weight
cgo_dot_radius sculpt_bond_weight
cgo_dot_width sculpt_field_mask
cgo_line_radius sculpt_hb_overlap
cgo_line_width sculpt_hb_overlap_base
cgo_ray_width_scale sculpt_line_weight
cgo_sphere_quality sculpt_max_max
cgo_transparency sculpt_max_min
clamp_colors sculpt_max_scale
connect_bonded sculpt_max_weight
connect_cutoff sculpt_memory
connect_mode sculpt_min_max
coulomb_cutoff sculpt_min_min
coulomb_dielectric sculpt_min_scale
coulomb_units_factor sculpt_min_weight
cull_spheres sculpt_nb_interval
[[Dash_Gap]] sculpt_plan_weight
[[Dash_Length]] sculpt_pyra_weight
[[Dash_Radius]] sculpt_tors_tolerance
[[Dash_Round_Ends]] sculpt_tors_weight
dash_width sculpt_tri_max
debug_pick sculpt_tri_min
defer_builds_mode sculpt_tri_mode
defer_updates sculpt_tri_scale
[[depth_cue]] sculpt_tri_weight
dihedral_label_position sculpt_vdw_scale
dihedral_size sculpt_vdw_scale14
direct sculpt_vdw_vis_max
dist_counter sculpt_vdw_vis_mid
distance_exclusion sculpt_vdw_vis_min
dot_color sculpt_vdw_vis_mode
dot_density sculpt_vdw_weight
dot_hydrogens sculpt_vdw_weight14
dot_lighting sculpting
dot_mode sculpting_cycles
dot_normals secondary_structure
dot_radius security
dot_solvent sel_counter
[[dot_width]] selection_overlay
draw_frames selection_round_points
editor_auto_dihedral selection_visible_only
editor_auto_origin [[selection_width]]
editor_label_fragments selection_width_max
fast_idle selection_width_scale
fetch_path [[seq_view]]
[[Field_Of_View]] seq_view_alignment
fit_iterations seq_view_color
fit_tolerance seq_view_discrete_by_state
float_labels seq_view_fill_char
[[fog]] seq_view_fill_color
[[fog_start]] seq_view_format
frame seq_view_label_color
full_screen seq_view_label_mode
gamma seq_view_label_spacing
gaussian_b_adjust seq_view_label_start
gaussian_b_floor [[seq_view_location]]
gaussian_resolution seq_view_overlay
gl_ambient seq_view_unaligned_color
h_bond_cone seq_view_unaligned_mode
h_bond_cutoff_center session_file
h_bond_cutoff_edge session_migration
h_bond_exclusion session_version_check
h_bond_max_angle [[shininess]]
h_bond_power_a show_alpha_checker
h_bond_power_b show_progress
[[half_bonds]] simplify_display_lists
hash_max single_image
hide_underscore_names slice_dynamic_grid
idle_delay slice_dynamic_grid_resolution
ignore_case slice_grid
ignore_pdb_segi slice_height_map
image_dots_per_inch slice_height_scale
internal_feedback slice_track_camera
[[Internal Gui|internal_gui]] slow_idle
internal_gui_control_size smooth_color_triangle
internal_gui_mode solvent_radius
internal_gui_width spec_count
[[internal_prompt]] spec_direct
isomesh_auto_state spec_direct_power
[[label_color]] spec_power
[[Label_font_id]] [[spec_reflect]]
[[Label_outline_color]] specular
[[label_position]] specular_intensity
[[label_shadow_mode]] [[sphere_color]]
[[label_size]] sphere_mode
legacy_mouse_zoom sphere_point_max_size
legacy_vdw_radii sphere_point_size
light sphere_quality
light2 [[sphere_scale]]
light3 sphere_solvent
light4 [[sphere_transparency]]
light5 spheroid_fill
light6 spheroid_scale
light7 spheroid_smooth
light8 ss_helix_phi_exclude
light9 ss_helix_phi_include
[[light_count]] ss_helix_phi_target
line_radius ss_helix_psi_exclude
[[line_smooth]] ss_helix_psi_include
line_stick_helper ss_helix_psi_target
line_width ss_strand_phi_exclude
log_box_selections ss_strand_phi_include
log_conformations ss_strand_phi_target
logging ss_strand_psi_exclude
matrix_mode ss_strand_psi_include
max_threads ss_strand_psi_target
max_triangles state
[[mesh_color]] static_singletons
[[mesh_lighting]] stereo
[[mesh_mode]] stereo_angle
mesh_normals stereo_double_pump_mono
[[mesh_quality]] stereo_mode
mesh_radius stereo_shift
mesh_solvent [[stick_ball]]
[[mesh_type]] [[stick_ball_ratio]]
[[mesh_width]] stick_color
[[min_mesh_spacing]] stick_fixed_radius
mouse_limit [[stick_nub]]
mouse_restart_movie_delay stick_overlap
mouse_scale stick_quality
mouse_selection_mode stick_radius
movie_delay [[stick_transparency]]
movie_loop stick_valence_scale
multiplex stop_on_exceptions
no_idle surface_best
nonbonded_size surface_carve_cutoff
normal_workaround surface_carve_selection
normalize_ccp4_maps surface_carve_state
normalize_grd_maps surface_circumscribe
normalize_o_maps surface_clear_cutoff
nvidia_bugs surface_clear_selection
opaque_background surface_clear_state
[[orthoscopic]] surface_color
overlay surface_debug
overlay_lines surface_miserable
pdb_conect_all surface_mode
pdb_discrete_chains surface_normal
pdb_echo_tags surface_optimize_subsets
pdb_hetatm_sort surface_poor
pdb_honor_model_number surface_proximity
pdb_insertions_go_first surface_quality
pdb_insure_orthogonal surface_ramp_above_mode
pdb_literal_names surface_solvent
pdb_no_end_record surface_trim_cutoff
pdb_reformat_names_mode surface_trim_factor
pdb_retain_ids surface_type
pdb_standard_order suspend_updates
pdb_truncate_residue_name swap_dsn6_bytes
pdb_unbond_cations sweep_angle
pdb_use_ter_records sweep_mode
[[pickable]] sweep_phase
png_file_gamma sweep_speed
png_screen_gamma test1
power test2
pqr_no_chain_id text
presentation texture_fonts
presentation_auto_quit [[transparency]]
presentation_auto_start transparency_mode
presentation_mode transparency_picking_mode
preserve_chempy_ids triangle_max_passes
pymol_space_max_blue trim_dots
pymol_space_max_green [[two_sided_lighting]]
pymol_space_max_red use_display_lists
pymol_space_min_factor [[valence]]
raise_exceptions valence_default
rank_assisted_sorts valence_size
ray_blend_blue validate_object_names
ray_blend_colors [[virtual_trackball]]
ray_blend_green wildcard
ray_blend_red wizard_prompt_mode
ray_color_ramps wrap_output

[[Category:Settings|All Settings]]

Practical Pymol for Beginners

2007-04-11T16:30:06Z

Oasisbob: /* Whoops: Getting unstuck */

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.

==The PyMol Interface==
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.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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 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:
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view.
* '''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.
* '''L''' - Label: Label atoms, residues, etc.
* '''C''' - Color: Change the color of atoms and groups.

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>''').

===About the command line===
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.

Although this guide may include some text commands and links to more advanced documentation, 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]''.

==Getting started: explore a protein==
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.

[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]
# 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]).
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines.
# 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.
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''.
# 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.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel.
#*Rota: Rotate
#*Move: Translate object along an axis
#*MoveZ: aka Zoom
#*Sele: Select`
#*Slab:
#*Cent:
#*PkAt:

==What else can this thing do?==
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.

===Saving an image===
You've found the perfect view, and you'd like to save it?

# 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.
#* For example, images for printing and presenting should be larger than images for a posting on a website.
# 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.
# 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.

'''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.

===Selecting parts of an object===
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.

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.

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.

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.

===Whoops: Getting unstuck===
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common problems:

* ''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.
* ''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.
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state, but all work will be lost.

==Coming Soon==
===Saving work===
===Scripting===
===Logging===

Practical Pymol for Beginners

2007-04-11T04:42:49Z

Oasisbob: /* Whoops: Getting unstuck */

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.

==The PyMol Interface==
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.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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 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:
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view.
* '''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.
* '''L''' - Label: Label atoms, residues, etc.
* '''C''' - Color: Change the color of atoms and groups.

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>''').

===About the command line===
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.

Although this guide may include some text commands and links to more advanced documentation, 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]''.

==Getting started: explore a protein==
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.

[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]
# 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]).
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines.
# 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.
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''.
# 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.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel.
#*Rota: Rotate
#*Move: Translate object along an axis
#*MoveZ: aka Zoom
#*Sele: Select`
#*Slab:
#*Cent:
#*PkAt:

==What else can this thing do?==
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.

===Saving an image===
You've found the perfect view, and you'd like to save it?

# 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.
#* For example, images for printing and presenting should be larger than images for a posting on a website.
# 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.
# 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.

'''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.

===Selecting parts of an object===
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.

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.

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.

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.

===Whoops: Getting unstuck===
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:

* ''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.
* ''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.
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.

==Coming Soon==
===Saving work===
===Scripting===
===Logging===

Practical Pymol for Beginners

2007-04-11T04:31:47Z

Oasisbob: /* Saving an image */

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.

==The PyMol Interface==
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.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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 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:
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view.
* '''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.
* '''L''' - Label: Label atoms, residues, etc.
* '''C''' - Color: Change the color of atoms and groups.

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>''').

===About the command line===
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.

Although this guide may include some text commands and links to more advanced documentation, 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]''.

==Getting started: explore a protein==
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.

[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]
# 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]).
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines.
# 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.
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''.
# 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.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel.
#*Rota: Rotate
#*Move: Translate object along an axis
#*MoveZ: aka Zoom
#*Sele: Select`
#*Slab:
#*Cent:
#*PkAt:

==What else can this thing do?==
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.

===Saving an image===
You've found the perfect view, and you'd like to save it?

# 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.
#* For example, images for printing and presenting should be larger than images for a posting on a website.
# 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.
# 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.

'''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.

===Selecting parts of an object===
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.

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.

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.

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.

===Whoops: Getting unstuck===
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:

* ''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.
* ''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.
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.

==Coming Soon==
===Saving work===
===Scripting===
===Logging===

Practical Pymol for Beginners

2007-04-11T04:25:37Z

Oasisbob:

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.

==The PyMol Interface==
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.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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 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:
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view.
* '''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.
* '''L''' - Label: Label atoms, residues, etc.
* '''C''' - Color: Change the color of atoms and groups.

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>''').

===About the command line===
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.

Although this guide may include some text commands and links to more advanced documentation, 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]''.

==Getting started: explore a protein==
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.

[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]
# 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]).
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines.
# 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.
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''.
# 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.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel.
#*Rota: Rotate
#*Move: Translate object along an axis
#*MoveZ: aka Zoom
#*Sele: Select`
#*Slab:
#*Cent:
#*PkAt:

==What else can this thing do?==
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.

===Saving an image===
You've found the perfect view, and you'd like to save it?

# 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.
#* For example, images for printing and presenting should be larger than images for a posting on a website.
# 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.
# 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.

'''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.

===Selecting parts of an object===
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.

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.

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.

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.

===Whoops: Getting unstuck===
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:

* ''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.
* ''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.
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.

==Coming Soon==
===Saving work===
===Scripting===
===Logging===

Talk:Practical Pymol for Beginners

2007-04-11T03:48:15Z

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...

This page is still in a work in progress. [[User:Oasisbob|Oasisbob]] 22:48, 10 April 2007 (CDT)

==TODO:==
* Capitalization for internal GUI features?
* Definition of an object?
* Objects vs selection objects?
* Pic of External GUI for command line
* s/PyMol/PyMOL
* Dummy-style advanced notation.
* Howto run commands...
** Tone change.
* intro and outro

Practical Pymol for Beginners

2007-04-11T03:47:27Z

Oasisbob:

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.

==The PyMol Interface==
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.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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 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:
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view.
* '''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.
* '''L''' - Label: Label atoms, residues, etc.
* '''C''' - Color: Change the color of atoms and groups.

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>''').

===About the command line===
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.

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]''.

==Getting started: explore a protein==
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.

[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]
# 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]).
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines.
# 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.
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''.
# 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.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel.
#*Rota: Rotate
#*Move: Translate object along an axis
#*MoveZ: aka Zoom

==What else is this thing good for?==
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.

===Saving an image===
You've found the perfect view, and you'd like to save it?

# 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.
#* For example, images for printing and presenting should be larger than images for a posting on a website.
# 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.
# 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.

'''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.

===Whoops: Getting unstuck===
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:

* ''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.
* ''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.
* ''Things are really messed up:'' Use '''File''', '''Reinitalize''' to reset PyMOL to its initial state.

Practical Pymol for Beginners

2007-04-11T03:29:56Z

Oasisbob: more changes

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.

==The PyMol Interface==
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.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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 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:
* '''A''' - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations
* '''S''' - Show: Change the way things appear, eg change to stick or cartoon view.
* '''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.
* '''L''' - Label: Label atoms, residues, etc.
* '''C''' - Color: Change the color of atoms and groups.

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>''').

===About the command line===
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.

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]''.

==Getting started: explore a protein==
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.

[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
# 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]).
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines.
# 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.
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''.
# 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.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel.
#*Rota: Rotate
#*Move: Translate object along an axis
#*MoveZ: aka Zoom

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.

==Saving an image==
You've found the perfect view, and you'd like to save it?

# 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.
#* For example, images for printing and presenting should be larger than images for a posting on a website.
# 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.
# 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.

'''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.

==Getting unstuck==
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:

* ''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.
* ''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.

==Other==
* Reinitialize hint

==TODO:==
* Capitalization for internal GUI features?
* Definition of an object?
* Objects vs selection objects?
* Pic of External GUI for command line
* s/PyMol/PyMOL
* Dummy-style advanced notation.
* Howto run commands...
** Tone change.
* intro and outro

File:Mouse-3view.png

2007-04-11T02:09:20Z

Oasisbob: Mouse button assignments for default 3-button viewing mode

Mouse button assignments for default 3-button viewing mode

Practical Pymol for Beginners

2007-04-10T21:55:57Z

Oasisbob: more text

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.

==The PyMol Interface==
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.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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:
* A - Actions: Close, etc
* S - Show: Change the way an object is represented, eg change stick view to cartoon view.
* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations.
* L - Label: Label atoms, residues, etc.
* C - Color: Change the color of atoms and groups.

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>''').

==About the command line==
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.

Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.

==Visualize a protein==
These instructions cover opening a PDB file and using PyMol as tool for molecular exploration.
[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
# 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]).
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines.
# 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.
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''.
# 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.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
# Click and drag the protein to change the view. Reminder: a legend for mouse actions is below the object control panel.
#*(Cover mouse matrix abbreviations)

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.

==Saving an image==
You've found the perfect view, and you'd like to save it?

# 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.
#* For example, images for printing and presenting should be larger than images for a posting on a website.
# 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.
# 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.

'''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.

==Getting unstuck==
PyMOL is a program meant to be explored and played with, and sometimes funny things happen in the process. A few common scenarios:

* ''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.
* ''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.

==Other==
* Reinitialize hint

==TODO:==
* Capitalization for internal GUI features?
* Definition of an object?
* Objects vs selection objects?
* Pic of External GUI for command line
* s/PyMol/PyMOL
* Dummy-style advanced notation.
* Howto run commands...
** Tone change.
* intro and outro

Practical Pymol for Beginners

2007-04-10T20:47:42Z

Oasisbob: added some images, still a work in progress...

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.

==About the command line==
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.

Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative, not required.

==About the viewer==
[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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:
* A - Actions: Close, etc
* S - Show: Change the way an object is represented, eg change stick view to cartoon view.
* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations.
* L - Label: Label atoms, residues, etc.
* C - Color: Change the color of atoms and groups.

==Visualize a protein==
These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this:
[[Image:Kchannel-rainbow.png|thumb|center|click to see full image]]
# 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.)
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks.
# 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.
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''Chainbows''' from the '''By Chain''' menu.
# Click and drag the protein to change the view. A legend for mouse actions is below the object control panel.
#*(Cover mouse matrix abbreviations)

==Save an image==
# 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.
#* Using the ''ray'' command before saving will draw a higher quality version of the molecule with shadows, etc.

==Other==
* Reinitialize hint

==TODO:==
* Capitalization for internal GUI features?
* Definition of an object?
* Objects vs selection objects?
* Pic of External GUI for command line

File:Viewer guide.png

2007-04-10T20:34:27Z

Oasisbob: A labeled legend of the PyMol interface.

A labeled legend of the PyMol interface.

File:Kchannel-rainbow.png

2007-04-10T20:03:38Z

Oasisbob: An example rendering of the K+ Channel from PDB 1BL8

An example rendering of the K+ Channel from PDB 1BL8

Practical Pymol for Beginners

2007-04-10T03:32:24Z

Oasisbob: /* Visualize a protein */

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.

==About the command line==
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.

Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.

==Visualize a protein==
These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this:
# 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.)
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks.
# 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:
#* A - Actions: Close, etc
#* S - Show: Change the way an object is represented, eg change stick view to cartoon view.
#* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations.
#* L - Label: Label atoms, residues, etc.
#* C - Color: Change the color of atoms and groups.
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''Chainbows''' from the '''By Chain''' menu.
# Click and drag the protein to change the view. A legend for mouse actions is below the command buttons.
# 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.
#* Using the ''ray'' command before saving will draw a higher quality version of the molecule with shadows, etc.

==Other==
* Reinitialize hint

Practical Pymol for Beginners

2007-04-10T03:30:06Z

Oasisbob:

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.

==About the command line==
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.

Although this guide may include some text commands (''like this''), they're purely optional and meant to be informative.

==Visualize a protein==
These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this:
# 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.)
# Open the PDB file using '''File''', '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as sticks.
# 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:
#* A - Actions: Close, etc
#* S - Show: Change the way an object is represented, eg change stick view to cartoon view.
#* H - Hide: Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' has commands for hiding unwanted representations.
#* L - Label: Label atoms, residues, etc.
#* C - Color: Change the color of atoms and groups.
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''Chainbows''' from the '''By Chain''' menu.
# Click and drag the protein to change the view. A legend for mouse actions is below the command buttons.
# 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.
#*

==Other==
* Reinitialize hint

Practical Pymol for Beginners

2007-04-10T03:04:52Z

Oasisbob: /* Visualize a protein */

Practical Pymol for Beginners

2007-04-10T02:49:59Z

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. ...

Category:Uncategorized

2007-04-10T02:05:27Z

Oasisbob: beginning pymol beginners tutorial

==Alter key bindings==
It's not GUI, but you could simply bind a function key such as F1 to a command:
<source lang="python">
cmd.set_key('F1',lambda :cmd.show('sticks'))
</source>

==Coloring Surface with Electrostatic Potential==
You have to load the potential data by Delphi or some other program like AMBER version 9:
<source lang="python">
load sample.pdb, molecule
load sample.delphi, potential
show surface, molecule
ramp_new level, potential, [-7,0,7]
set surface_color, level, molecule
</source>

==Van der Waals radii==
van der Waals Radii are hard coded in Pymol.
They may be obtained for given atoms from:
<source lang="python">
iterate (name C), print vdw
</source>
Default values are:
*C : 1.70
*O : 1.52
*N : 1.55
*H : 1.20
*P : 1.80

and may be changed with the command [[alter]]

==Tutorial for Beginners==
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.