PyMOL Wiki - User contributions [en]

Feedback

2006-08-28T16:52:14Z

AdShea: Fixed code section

==DESCRIPTION==

"feedback" allows you to change the amount of information output by pymol.

==USAGE==
feedback action,module,mask

*action is one of ['set','enable','disable']
*module is a space-separated list of strings or simply "all"
*mask is a space-separated list of strings or simply "everything"

==NOTES==
"feedback" alone will print a list of the available module choices

==PYMOL API==
<source lang="python">
cmd.feedback(string action,string module,string mask)
</source>

==EXAMPLES==
feedback enable, all , debugging
feedback disable, selector, warnings actions
feedback enable, main, blather

[[Category:Commands|feedback]]

Feedback

2006-08-28T16:51:26Z

AdShea: Created Page

==DESCRIPTION==

"feedback" allows you to change the amount of information output by pymol.

==USAGE==
feedback action,module,mask

*action is one of ['set','enable','disable']
*module is a space-separated list of strings or simply "all"
*mask is a space-separated list of strings or simply "everything"

==NOTES==
"feedback" alone will print a list of the available module choices

==PYMOL API==
<source lang="python">
cmd.feedback(string action,string module,string mask)
</source>

==EXAMPLES==
<code>
feedback enable, all , debugging
feedback disable, selector, warnings actions
feedback enable, main, blather
</code>

[[Category:Commands|feedback]]

Full Screen

2006-08-28T16:42:39Z

AdShea: Added Python command

===DESCRIPTION===
'''full_screen''' enables or disables PyMOL's full screen mode. This does not work well on all platforms.

===USAGE===
full_screen on
full_screen off

<source lang="python">
cmd.full_screen('on')
cmd.full_screen('off')
</source>

[[Category:Commands|full_screen]]

Talk:Set View

2006-08-08T20:53:20Z

AdShea: about orthoscopic flag

I've edited the description to reflect the broken flag at index 17, if there's just something I missed, or if it gets fixed, please edit it back --[[User:AdShea|AdShea]] 15:53, 8 Aug 2006 (CDT)

Set View

2006-08-08T20:51:58Z

AdShea: Description of the view matrix. Including broken orthoscopic view flag

===DESCRIPTION===
'''set_view''' sets viewing information for the current scene, including the rotation matrix, position, origin of rotation, clipping planes, and the orthoscopic flag.

===USAGE===
set_view (...) where ... is 18 floating point numbers

===PYMOL API===
<source lang="python">
cmd.set_view(string-or-sequence view)
</source>

===NOTES===
Contents of the view matrix
*0 - 8 = 3x3 rotation matrix which transforms model to camera space
*9 - 11 = camera position (in model space and relative to the origin of rotation)
*12 - 14 = origin of rotation (in model space)
*15 = front plane distance from the camera
*16 = rear plane distance from the camera
*17 = not implemented (the online help says that this should be the orthoscopic view flag, but PyMol as of v0.99 does not implement this)

===SEE ALSO===
[[Get View]]

[[Category:Commands|set_view]]

Main Page

2006-08-08T15:49:14Z

AdShea: Added PyMol Settings to the Links of Interest so it's still around when it get's bumped off the news

* [[TOPTOC|'''Table of Contents''']]
 
* [[Special:Allpages|Alphabetized Index of all pages]]
 

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

== New Users ==
The PyMol Wiki actively seeks new users and contributors! However, due to massive amount of spamming, we've changed the registration process, until further notice. '''If you would like access,''' you will need to be verified by a system administrator/sysop. To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol). Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''. Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.

==News==
===PyMol===
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.
* New cool [[ray]] tracing features added!

===Wiki===
* [[SURFNET]] information on reading surfaces from other programs added.
* Two new [[:Category:Plugins|Plugins]] have been added, [[NsSNP Loader]] and [[Proxy Config]].
* Added a page that lists all [[Settings|PyMol settings]]. We need to start documenting these.
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established.
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.

===News Archive===
*See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[Settings|PyMol Settings]]
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

Settings

2006-08-02T20:33:59Z

AdShea: Updated the count at the top

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_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]]

Set View

2006-08-01T16:24:34Z

AdShea: Fixed link

Get View

2006-08-01T16:24:09Z

AdShea: Fixed link

===DESCRIPTION===
'''get_view''' returns and optionally prints out the current view information in a format which can be embedded into a command script and can be used in subsequent calls to '''set_view'''.

If a log file is currently open, get_view will not write the view matrix to the screen unless the "output" parameter is 2.

===USAGE===
get_view

===PYMOL API===
<source lang="python">
cmd.get_view(output=1,quiet=1)

my_view= cmd.get_view()
</source>

output control:
*0 = output matrix to screen
*1 = don't output matrix to screen
*2 = force output to screen even if log file is open
*3 = return formatted string instead of a list

===API USAGE===
<source lang="python">
cmd.get_view(0) # zero option suppresses output (LEGACY approach)
cmd.get_view(quiet=1) # suppresses output using PyMOL's normal "quiet" parameter.
</source>

===NOTES===
Contents of the view matrix
*0 - 8 = 3x3 rotation matrix which transforms model to camera space
*9 - 11 = camera position (in model space and relative to the origin of rotation)
*12 - 14 = origin of rotation (in model space)
*15 = front plane distance from the camera
*16 = rear plane distance from the camera
*17 = orthoscopic flag

===SEE ALSO===
[[Set View]]

[[Category:Commands|get_view]]

Get View

2006-08-01T16:23:33Z

AdShea:

Depth cue

2006-07-27T15:11:03Z

AdShea: Added Example Images

== Overview ==
Sets whether or not PyMol overlays a 'fog' on objects farther away from the camera to assist in emphasizing what is in the foreground of the image.

== Syntax ==
<source lang="python">
set depth_cue, 1 # turn on depth cueing
set depth_cue, 0 # turn off depth cueing
</source>

==Example==
{| border="0" cellspacing="0" cellpadding="5" align="center"
|[[Image:DepthCue0.png|thumb|frame|depth_cue=0]]
|[[Image:DepthCue1.png|thumb|frame|depth_cue=1]]
|}
== See Also ==
[[fog]], [[Ray_Trace_Fog]], [[Field_Of_View]]

File:DepthCue1.png

2006-07-27T15:05:42Z

AdShea: Example with depth_cue=1

Example with depth_cue=1

File:DepthCue0.png

2006-07-27T15:04:43Z

AdShea: Example with depth_cue=0

Example with depth_cue=0

Talk:Spec reflect

2006-07-25T15:07:02Z

AdShea:

Talk:Spec reflect

2006-07-24T14:01:47Z

AdShea:

The example images should tell what settings were used in the caption.

Spec reflect

2006-07-24T14:00:55Z

AdShea: Changed Ex -> Example

== Overview ==
This setting changes how PyMol handles specular reflections. Essentially, this setting, when combined with [[spec_power]] adjusts how sharp or diffuse the reflection is, giving you shiny looking surface or duller surfaces.

== Syntax ==
<source lang="python">
set spec_reflect, 2
set spec_power, 1500
</source>

== Examples ==
<gallery>
Image:Spec.png|Specular Reflection Example
Image:Spec1.png|Specular Reflection Example
</gallery>

== See Also ==
* [[spec_power]]
* [http://en.wikipedia.org/wiki/Specular_reflection About Specular Reflections]
* [http://www.glenbrook.k12.il.us/gbssci/phys/class/refln/u13l1d.html More About Specular Reflections]

Iterate State

2006-07-06T12:39:58Z

AdShea: Made this useful

===DESCRIPTION===
Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position of the current atom. One common usage is to extract the positions as a python list to alter then write back to the molecule using alter_state.

===USAGE===
iterate_state state,(selection),expression

===EXAMPLES===
==From PyMOL command line==
To get the sum of x coordinates:
<source lang="python">
stored.sum_x = 0.0
iterate_state 1,(all),stored.sum_x = stored.sum_x + x
</source>
To get a list of the positions in a selection
<source lang="python">
stored.pos = []
iterate_state 1, (all), stored.pos.append((x,y,z))
</source>
==From Python==
To get a list of positions
<source lang="python">
stored.pos = []
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')
</source>

===SEE ALSO===
[[Cmd iterate]], [[Cmd alter]], [[Cmd alter_state]]

[[Category:Commands|iterate_state]]

Settings

2006-06-26T19:11:31Z

AdShea: added line_smooth

These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 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_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]]

Talk:Line smooth

2006-06-26T19:10:50Z

AdShea: note at creation

This page could use some example pictures, I don't have pymol on this computer though.

Talk:Main Page

2006-06-08T12:43:18Z

AdShea: /* Where is the anti-spam mechanism/strategy? */

== New ==

=== Some Thoughts For Discussion ===
* We need to accurately document settings for PyMol. This would greatly improve the value of the site. We should also provide images and examples.

* Would it be helpful to get rid of display of the somewhat awkward "Cmd" prefix for commands, and simply do a better job of separating the sections that cover concepts and ideas from those that discuss specific commands?

* Empty links discourage. Could we eliminate them sooner rather than later? Yes, they are helpful initially for maintaining some structure, but people do get bummed out when they follow a link for an interesting topic and end up with nothing. If there are too many of these, then they may quit and go home before finding the real content -- and that would be a shame since there is now plenty of real content.

* For those coming into the Wiki for the first time, we should insure that the most useful content is out front and on top. Right now the TOC has an awful lot of blank links, so having it on top isn't so helpful as a starting point for nagivation. In contrast, the Categories, Script Library, and PyMOL Commands sections all seem like pretty good starting points.

* For people (like me) who don't know the first thing about Wiki's, more "newbies click here to learn" links would help ease the transition...

* Categories & subcategories confuse me. The resulting titles baffle. For example, '''Category: Using Pymol Objects and Selections Working with Objects'''. Shouldn't there be another colon in there? '''Category: Using Pymol Objects and Selections: Working with Objects''' Is this just a Wiki thing?

[[User:Warren|Warren]] (BTW: Please don't weight what I write too heavily here. With respect to PyMolWiki, I am just another user -- and a clueless one at that).
----
=====Begin Inchoate's Comments To Warren=====
First off, thanks for the post. I always welcome better ways to work and organize information. I don't claim to know any more than anyone else, I just took the initiative for PyMolWiki.

Warren, you're completely right. Something needs to change, to make this more usable for people. I tried to organize the PyMol information via the user manual and user comments. Imposing a hierarchy on a system that doesn't really want one, isn't such a good idea, or my imposition was implemented incorrectly. The link names need to be MUCH shorter: take a look at http://wikipedia.org. They have 500,000+ pages and they have short link names. I tried to make a hierarchy so that if three such people come in and look up "rotate" that they go to the right page. That is, there's "rotate," "cmd.rotate," and camera independent rotations and whatnot. We have name ambiguitities. Do we just make one big page with "rotate" and include all its information there, or do we make "rotate" a category and dole out the pages to the category?

I'm ambivalent towards empty links. They remind me of what basic concepts that need filling, but are annoying if you're searching for info. and there's nothing there.

As far as the comments on categories and subcategories, as I understand it, you can't use double ":"s in names. You have categories and then something is made a subcategory by claiming that is'a category of a category. Kinda' strange.

I do think organization is good. My way was seemingly obfuscated. Don't you think PyMol commands should somehow be lumped into available categories?
Changes to be made from my POV:
* Much shorter link names
* Kill the hierarchy?
* How to use the Wiki Intro

======Part 2======
I tihnk I found the problem, and I might be able to solve it. I just made things hard by including the hierarchy in the naming scheme, when that's not appropriate. I think the hierarchy's still very important; however, I think the name-ambiguity problem is not solved via this method.

======Part 3======
I've made lots of changes:
* I actually took Warren's suggestion on epmty links. I sifted through the TOPTOC and made empty links normal text -- but left them there in case anyone wants to make them links by adding content.
* Also, I've gone through all the commands and removed the Cmd prefix. The commands, and all commands buried in modules should be easy to create by simply making a new page as, for example, "Editing.Get_Dihedral" or whatever.
* The names of the links should be MUCH easier to handle, and are far less obfuscated.

MediaWiki-style organization is starting to make sense. :-)

[[User:Inchoate|Inchoate]] 00:48, 6 May 2005 (CDT)
----

=====A singular vote from TStout=====

One thing that I think has been missing from the manuals and the Wiki (and manuals for many other programs, I might add) are copious EXAMPLES of how to actually use a command. Speaking as an advanced-dummy, I find it terribly imposing to be presented with something like '''"cmd.select(string name, string selection)"''' as an explanation for how a command works. "How does that translate into what I should type?" is the polite version of how I end up reading such things.... :) Recently, I have noticed more "real" examples being entered into the Wiki: THANK YOU! The example given just now also comes complete with an Examples entry with things like:
select near , (ll expand 8)
select near , (ll expand 8)
select bb, (name ca,n,c,o )
For beginning users, such entries are invaluable. In fact, I would extend that to say that an inverted approach to manual/Wiki writing would be even better for the beginning PyMOL user: organize around how to accomplish the usual tasks, not around a glossary of all the possible commands......That said, a HUGE thank you to all who are putting in so much time building, maintaining and getting this to critical mass so that it becomes the invaluable resource it clearly is headed toward! -Tom

----

=====Where is the anti-spam mechanism/strategy?=====
Manual removing spam contents really sucks.
----
Edit by AdShea
One good strategy is to search all namespaces for 'http' (without the quotes). This will show links containing that string, which should catch any spam links.

== cmd commands ==

Hi Inchoate

I tried to change the "cmd delete" command into "delete", I moved the page but I couldn't figure out how to change the command name in the command list page...
Any help is welcome! I'm a newbie with Wiki...
Cheers

----
Edit:
Ok now it's gone... Anyway if you want to post the answer I could need it in the future!!

----
Edit (by Inchoate)
Glad you got it -- or someone got it. Didn't see this message until too late.

---
Reply by AdShea
The Commands page is an automatically generated list of pages in the command category. Any time you move or or add a page in that category, it goes on the list.

Talk:Main Page

2006-06-08T12:39:16Z

AdShea: /* cmd commands */

== New ==

=== Some Thoughts For Discussion ===
* We need to accurately document settings for PyMol. This would greatly improve the value of the site. We should also provide images and examples.

* Would it be helpful to get rid of display of the somewhat awkward "Cmd" prefix for commands, and simply do a better job of separating the sections that cover concepts and ideas from those that discuss specific commands?

* Empty links discourage. Could we eliminate them sooner rather than later? Yes, they are helpful initially for maintaining some structure, but people do get bummed out when they follow a link for an interesting topic and end up with nothing. If there are too many of these, then they may quit and go home before finding the real content -- and that would be a shame since there is now plenty of real content.

* For those coming into the Wiki for the first time, we should insure that the most useful content is out front and on top. Right now the TOC has an awful lot of blank links, so having it on top isn't so helpful as a starting point for nagivation. In contrast, the Categories, Script Library, and PyMOL Commands sections all seem like pretty good starting points.

* For people (like me) who don't know the first thing about Wiki's, more "newbies click here to learn" links would help ease the transition...

* Categories & subcategories confuse me. The resulting titles baffle. For example, '''Category: Using Pymol Objects and Selections Working with Objects'''. Shouldn't there be another colon in there? '''Category: Using Pymol Objects and Selections: Working with Objects''' Is this just a Wiki thing?

[[User:Warren|Warren]] (BTW: Please don't weight what I write too heavily here. With respect to PyMolWiki, I am just another user -- and a clueless one at that).
----
=====Begin Inchoate's Comments To Warren=====
First off, thanks for the post. I always welcome better ways to work and organize information. I don't claim to know any more than anyone else, I just took the initiative for PyMolWiki.

Warren, you're completely right. Something needs to change, to make this more usable for people. I tried to organize the PyMol information via the user manual and user comments. Imposing a hierarchy on a system that doesn't really want one, isn't such a good idea, or my imposition was implemented incorrectly. The link names need to be MUCH shorter: take a look at http://wikipedia.org. They have 500,000+ pages and they have short link names. I tried to make a hierarchy so that if three such people come in and look up "rotate" that they go to the right page. That is, there's "rotate," "cmd.rotate," and camera independent rotations and whatnot. We have name ambiguitities. Do we just make one big page with "rotate" and include all its information there, or do we make "rotate" a category and dole out the pages to the category?

I'm ambivalent towards empty links. They remind me of what basic concepts that need filling, but are annoying if you're searching for info. and there's nothing there.

As far as the comments on categories and subcategories, as I understand it, you can't use double ":"s in names. You have categories and then something is made a subcategory by claiming that is'a category of a category. Kinda' strange.

I do think organization is good. My way was seemingly obfuscated. Don't you think PyMol commands should somehow be lumped into available categories?
Changes to be made from my POV:
* Much shorter link names
* Kill the hierarchy?
* How to use the Wiki Intro

======Part 2======
I tihnk I found the problem, and I might be able to solve it. I just made things hard by including the hierarchy in the naming scheme, when that's not appropriate. I think the hierarchy's still very important; however, I think the name-ambiguity problem is not solved via this method.

======Part 3======
I've made lots of changes:
* I actually took Warren's suggestion on epmty links. I sifted through the TOPTOC and made empty links normal text -- but left them there in case anyone wants to make them links by adding content.
* Also, I've gone through all the commands and removed the Cmd prefix. The commands, and all commands buried in modules should be easy to create by simply making a new page as, for example, "Editing.Get_Dihedral" or whatever.
* The names of the links should be MUCH easier to handle, and are far less obfuscated.

MediaWiki-style organization is starting to make sense. :-)

[[User:Inchoate|Inchoate]] 00:48, 6 May 2005 (CDT)
----

=====A singular vote from TStout=====

One thing that I think has been missing from the manuals and the Wiki (and manuals for many other programs, I might add) are copious EXAMPLES of how to actually use a command. Speaking as an advanced-dummy, I find it terribly imposing to be presented with something like '''"cmd.select(string name, string selection)"''' as an explanation for how a command works. "How does that translate into what I should type?" is the polite version of how I end up reading such things.... :) Recently, I have noticed more "real" examples being entered into the Wiki: THANK YOU! The example given just now also comes complete with an Examples entry with things like:
select near , (ll expand 8)
select near , (ll expand 8)
select bb, (name ca,n,c,o )
For beginning users, such entries are invaluable. In fact, I would extend that to say that an inverted approach to manual/Wiki writing would be even better for the beginning PyMOL user: organize around how to accomplish the usual tasks, not around a glossary of all the possible commands......That said, a HUGE thank you to all who are putting in so much time building, maintaining and getting this to critical mass so that it becomes the invaluable resource it clearly is headed toward! -Tom

----

=====Where is the anti-spam mechanism/strategy?=====
Manual removing spam contents really sucks.
----

== cmd commands ==

Hi Inchoate

I tried to change the "cmd delete" command into "delete", I moved the page but I couldn't figure out how to change the command name in the command list page...
Any help is welcome! I'm a newbie with Wiki...
Cheers

----
Edit:
Ok now it's gone... Anyway if you want to post the answer I could need it in the future!!

----
Edit (by Inchoate)
Glad you got it -- or someone got it. Didn't see this message until too late.

---
Reply by AdShea
The Commands page is an automatically generated list of pages in the command category. Any time you move or or add a page in that category, it goes on the list.

Sync

2006-06-05T20:05:01Z

AdShea: Created from source inline documentation

===DESCRIPTION===
"sync" is an API-only function which waits until all current commmands have been executed before returning. A timeout can be used to insure that this command eventually returns.

===PYMOL API===

cmd.sync(float timeout=1.0,float poll=0.05)

SEE ALSO
[[frame]]

[[Category:Commands|system]]

System

2006-06-05T19:55:29Z

AdShea: added category label

===DESCRIPTION===
"system" executes a command in a subshell under Unix or Windows.

===USAGE===
system command

===PYMOL API===
cmd.system(string command,int sync=1)

===NOTES===
async can only be specified from the Python level (not the command language)
*if async is 0 (default), then the result code from "system" is returned in r
*if async is 1, then the command is run in a separate thread whose object is returned

===SEE ALSO===
[[ls]], [[cd]], [[pwd]]

[[Category:Commands|system]]

System

2006-06-05T19:54:19Z

AdShea: copy from pymol help

===DESCRIPTION===

"system" executes a command in a subshell under Unix or Windows.

===USAGE===

system command

===PYMOL API===

cmd.system(string command,int sync=1)

===NOTES===

async can only be specified from the Python level (not the command language)
*if async is 0 (default), then the result code from "system" is returned in r
*if async is 1, then the command is run in a separate thread whose object is returned

===SEE ALSO===

[[ls]], [[cd]], [[pwd]]

Rebuild

2006-06-05T19:52:04Z

AdShea: liked refresh

===DESCRIPTION===
'''rebuild''' forces PyMOL to recreate geometric objects in case any of them have gone out of sync.

===USAGE===
rebuild [selection [, representation ]]

===PYMOL API===
<source lang="python">
cmd.rebuild(string selection = 'all', string representation = 'everything')
</source>

===SEE ALSO===
[[refresh]]

[[Category:Commands|rebuild]]

PyMOLWiki talk:Community Portal

2006-06-05T19:51:13Z

AdShea: removed spam

Talk:TOPTOC

2006-06-05T19:50:59Z

AdShea: removed spam

Talk:DynoPlot

2006-06-05T19:49:55Z

AdShea: removed spam

Talk:Nmr cnstr

2006-06-05T19:49:08Z

AdShea: removed spam

Hi,
is this for only one molecule or more?

Settings

2006-06-02T18:26:18Z

AdShea:

These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 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_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]]

Cartoon Helix Settings

2006-06-02T18:24:47Z

AdShea:

==Overview==
These are display settings.

These settings set the style in which cartoon helices are rendered. The default is a helix with an ellipsoid cross section. Fancy mode helices are ribbons with tubular edges à la MolScript. Cylindicial mode renders helices as solid cylinders.

==Syntax==
To turn on Fancy Helices:
set cartoon_fancy_helices, 1

To turn on Cylindrical Helices:
set cartoon_cylindrical_helices, 1

To return to default helices:
set cartoon_fancy_helices, 0
set cartoon_cylindrical_helices, 0

==Result==
{| border="0" cellspacing="0" cellpadding="5" align="center"
|[[image:Fancy.JPG|frame|Fancy helix|center]]
|[[image:Cylindre.JPG|frame|Cylindrical helix|center]]
|[[image:default.JPG|frame|Default representation|center]]
|}

Cartoon cylindrical helices

2006-06-02T18:22:16Z

AdShea: Redirect to helix settings

#REDIRECT [[Cartoon Helix Settings]]

Cartoon Helix Settings

2006-06-02T18:21:36Z

AdShea: Edited for cylinders and fancy

==Overview==
These are display settings.

These settings set the style in which cartoon helices are rendered. The default is a helix with an ellipsoid cross section. Fancy mode helices are ribbons with tubular edges à la MolScript. Cylindicial mode renders helices as solid cylinders.

==Syntax==
To turn on Fancy Helices:
set cartoon_fancy_helices, 1

To turn on Cylindrical Helices:
set cartoon_cylindrical_helices, 1

To return to default helices:
set cartoon_fancy_helices, 0
set cartoon_cylindrical_helices, 0

==Result==
[[image:Fancy.JPG|frame|Fancy helix|left]]
[[image:Cylindre.JPG|frame|Cylindrical helix|center]]
[[image:default.JPG|frame|Default representation|right]]

Cartoon fancy helices

2006-06-02T18:14:42Z

AdShea: Cartoon fancy helices moved to Cartoon Helix Settings

#REDIRECT [[Cartoon Helix Settings]]

User talk:Philaltist

2006-06-02T17:21:28Z

AdShea:

Do you think that a singe page for all the cartoon_helix types would be better than separate pages? e.g. putting the fance, normal, and cylindrical all on one page --Adam Shea

Redo

2006-06-02T14:03:16Z

AdShea: Fixing Names

===DESCRIPTION===
'''redo''' reapplies the conformational change of the object currently being edited.

===USAGE===
redo

===SEE ALSO===
[[Undo]], [[Push undo]]

[[Category:Commands|redo]]

Undo

2006-06-02T14:02:52Z

AdShea:

===DESCRIPTION===
'''undo''' restores the previous conformation of the object currently being edited.

===USAGE===
undo

===SEE ALSO===
[[Redo]], [[Push undo]]

[[Category:Commands|undo]]

Push Undo

2006-06-02T14:02:23Z

AdShea: Fixing Names

===DESCRIPTION===
'''push_undo''' stores the currently conformations of objects in the selection onto their individual kill rings.

===USAGE===
push_undo (all)

===SEE ALSO===
[[Undo]], [[Redo]]

[[Category:Commands|push_undo]]

Cmd undo

2006-06-02T14:01:28Z

AdShea: Cmd undo moved to Undo

#REDIRECT [[Undo]]

Undo

2006-06-02T14:01:09Z

AdShea: Just fixing Names

===DESCRIPTION===
'''undo''' restores the previous conformation of the object currently being edited.

===USAGE===
undo

===SEE ALSO===
[[Redo]], [[Push_undo]]

[[Category:Commands|undo]]

Settings

2006-06-01T12:48:40Z

AdShea:

These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 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_trace_mode
cache_frames ray_trace_slope_factor
cache_memory ray_transparency_contrast
[[cartoon_color]] ray_transparency_shadows
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_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]]

File:Default sheet.JPG

2006-06-01T12:47:25Z

AdShea: Sheets with option cartoon_fancy_sheet off

Sheets with option cartoon_fancy_sheet off

File:Fancy sheet.JPG

2006-06-01T12:46:57Z

AdShea: Sheets with option cartoon_fancy_sheet on

Sheets with option cartoon_fancy_sheet on

Cartoon fancy sheets

2006-06-01T12:45:02Z

AdShea:

==Overview==
This is a display setting.

This setting turns on and off the arrows at the end of sheets. The arrows point towards the C-terminus of the sheet. The default setting is on.

==Syntax==
Turn on:
set cartoon_fancy_sheets, 1

Turn off:
set cartoon_fancy_sheets, 0

==Result==
[[image:Fancy_sheet.JPG|frame|Fancy Sheets|left]]
[[image:default_sheet.JPG|frame|Plain Sheets|center]]

Cartoon Helix Settings

2006-06-01T12:38:16Z

AdShea: Fixed &agrave

==Overview==
This is a display setting.

It acts on the section of cartoon-represented helices. When turned off, the section is an ellipsoid. When turned on, the section is a line with circles on each end. The resulting helices are pretty slick ribbons with tubular edges à la MolScript.

==Syntax==
Turn on:
set cartoon_fancy_helices, 1

Turn off:
set cartoon_fancy_helices, 0

==Result==
[[image:Fancy.JPG|frame|fancy helices|left]]
[[image:default.JPG|frame|default representation|center]]

Settings

2006-05-31T21:54:37Z

AdShea: Deleted duplicate list

These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 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_trace_mode
cache_frames ray_trace_slope_factor
cache_memory ray_transparency_contrast
[[cartoon_color]] ray_transparency_shadows
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_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]]

Category:Script Library

2006-05-31T14:38:05Z

AdShea:

* [[Process_All_Files_In_Directory]] -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).

* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

* [[grepsel]] -- Make named selections using regular expressions (protein sequence).

* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.

[[Category:Scripting|Script Library]]

PythonTerminal

2006-05-31T14:37:39Z

AdShea:

===DESCRIPTION===
This is a small script to allow the execution of python commands from the PyMOL command line. It is very useful for both debugging, and for discovering new functions.

===USAGE===
<source lang="python">
py (python commands)
</source>

<source lang="python">
from pymol import cmd

def parse(command):
exec command

cmd.extend('py', parse)
</source>
[[Category:Script_Library]]

PythonTerminal

2006-05-31T14:36:55Z

AdShea:

===DESCRIPTION===
This is a small script to allow the execution of python commands from the PyMOL command line. It is very useful for both debugging, and for discovering new functions.

===USAGE===
py <python commands>

<source lang="python">
from pymol import cmd

def parse(command):
exec command

cmd.extend('py', parse)
</source>
[[Category:Script_Library]]

PythonTerminal

2006-05-31T14:34:35Z

AdShea:

This is a small script to allow the execution of python commands from the PyMOL command line. It is very useful for both debugging, and for discovering new functions.

<source lang="python">
from pymol import cmd

def parse(command):
exec command

cmd.extend('py', parse)
</source>
[[Category:Script_Library]]