https://wiki.pymol.org/api.php?action=feedcontributions&user=Dan&feedformat=atomPyMOL Wiki - User contributions [en]2024-03-28T14:47:54ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=User:Dan&diff=3020User:Dan2008-11-28T22:31:45Z<p>Dan: </p>
<hr />
<div>Hi!<br />
<br />
I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].<br />
<br />
My website is [http://metadatabase.org MetaBase]<br />
<br />
<br />
<br />
== Useful links ==<br />
* [[:Category:Commands]]<br />
* [[:Category: Settings]]<br />
<br />
<br />
Template for documentation of commands / settings<br />
<pre><br />
===DESCRIPTION===<br />
'''bold name''' description<br />
<br />
===USAGE===<br />
command line usage<br />
<br />
===PYMOL API===<br />
api usage<br />
<br />
===EXAMPLES===<br />
example usage<br />
<br />
===NOTES===<br />
Other stuff<br />
<br />
===SEE ALSO===<br />
Related stuff<br />
</pre></div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8530Rasmolify2008-02-22T13:51:14Z<p>Dan: </p>
<hr />
<div>Here it is! Long awaited, less tested;<br />
<br />
== Install ==<br />
; Linux : In your ~/.pymolrc set something like the following <PRE> run ~/pymolscripts/rasmolify.py </PRE> Finally, make a directory called ~/pymolscripts and copy the code below into a file called rasmolify.py - That should do the trick. You may also like to add a line that reads <PRE>set virtual_trackball, off</PRE> in your ~/.pymolrc<br />
<br />
; Windows : ???<br />
<br />
== Usage ==<br />
Think 'rasmol'<br />
<br />
== Related ==<br />
* http://arcib.dowling.edu/sbevsl/<br />
<br />
== TODO ==<br />
* Check if a 'selection' exists, and limit commands to that selection (map the concept of a rasmol 'selection' onto the concept of a pymol selection).<br />
* Implement 'scaling' units for display functions<br />
* Fix the mouse behaviour?<br />
* Add a rasmol GUI!<br />
<br />
== Code ==<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/1<br />
<br />
<br />
## Turn off the virtual_trackball<br />
cmd.set("virtual_trackball", "off")<br />
<br />
<br />
## spacefill<br />
def spacefill(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("spheres")<br />
elif(p1==''):<br />
cmd.show("spheres")<br />
else:<br />
print("feh!")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("cartoon")<br />
elif(p1==''):<br />
cmd.show("cartoon")<br />
else:<br />
print("feh!")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("lines")<br />
elif(p1==''):<br />
cmd.show("lines")<br />
else:<br />
print("feh!")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
</source><br />
<br />
[[Category:Script_Library]]</div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8529Rasmolify2008-02-22T13:49:37Z<p>Dan: </p>
<hr />
<div>Here it is! Long awaited, less tested;<br />
<br />
== Install ==<br />
; Linux : In your ~/.pymolrc set something like the following <PRE> run ~/pymolscripts/rasmolify.py </PRE> Finally, make a directory called ~/pymolscripts and copy the code below into a file called rasmolify.py - That should do the trick. You may also like to add a line that reads <PRE>set virtual_trackball, off</PRE> in your ~/.pymolrc<br />
<br />
; Windows : ???<br />
<br />
== Usage ==<br />
Think 'rasmol'<br />
<br />
== Related ==<br />
* http://arcib.dowling.edu/sbevsl/<br />
<br />
== TODO ==<br />
* Implement 'scaling' units for display functions<br />
* Fix the mouse behaviour?<br />
* Add a rasmol GUI!<br />
<br />
== Code ==<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/1<br />
<br />
<br />
## Turn off the virtual_trackball<br />
cmd.set("virtual_trackball", "off")<br />
<br />
<br />
## spacefill<br />
def spacefill(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("spheres")<br />
elif(p1==''):<br />
cmd.show("spheres")<br />
else:<br />
print("feh!")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("cartoon")<br />
elif(p1==''):<br />
cmd.show("cartoon")<br />
else:<br />
print("feh!")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("lines")<br />
elif(p1==''):<br />
cmd.show("lines")<br />
else:<br />
print("feh!")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
</source><br />
<br />
[[Category:Script_Library]]</div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8528Rasmolify2008-02-22T13:47:48Z<p>Dan: </p>
<hr />
<div>Here it is! Long awaited, less tested;<br />
<br />
== Install ==<br />
; Linux : In your ~/.pymolrc set something like the following <PRE> run ~/pymolscripts/rasmolify.py </PRE> Finally, make a directory called ~/pymolscripts and copy the code below into a file called rasmolify.py - That should do the trick. You may also like to add a line that reads <PRE>set virtual_trackball, off</PRE> in your ~/.pymolrc<br />
<br />
; Windows : ???<br />
<br />
== Usage ==<br />
Think 'rasmol'<br />
<br />
== Code ==<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/1<br />
<br />
<br />
## Turn off the virtual_trackball<br />
cmd.set("virtual_trackball", "off")<br />
<br />
<br />
## spacefill<br />
def spacefill(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("spheres")<br />
elif(p1==''):<br />
cmd.show("spheres")<br />
else:<br />
print("feh!")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("cartoon")<br />
elif(p1==''):<br />
cmd.show("cartoon")<br />
else:<br />
print("feh!")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(p1=''):<br />
if(p1=='off'):<br />
cmd.hide("lines")<br />
elif(p1==''):<br />
cmd.show("lines")<br />
else:<br />
print("feh!")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
</source><br />
<br />
[[Category:Script_Library]]</div>Danhttps://wiki.pymol.org/index.php?title=Category:Settings&diff=3788Category:Settings2008-02-22T13:25:38Z<p>Dan: </p>
<hr />
<div>== Introduction ==<br />
PyMol has over 500 settings! Everything from ray tracing fog, to perspective viewing, stereo rendering, colors, textures, memory settings and '''many''' more!<br />
<br />
One of the most powerful features is the amount of detail and control PyMOL offers through these various settings.<br />
<br />
For more information see [[Settings]].</div>Danhttps://wiki.pymol.org/index.php?title=Settings&diff=10142Settings2008-02-22T13:25:11Z<p>Dan: made a link a bit more explicit</p>
<hr />
<div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 43 done, 475 to go! See also [[:Category:Settings]]<br />
<br />
active_selections ray_default_renderer <br />
[[all_states]] ray_direct_shade <br />
[[ambient]] ray_hint_camera <br />
angle_label_position ray_hint_shadow <br />
angle_size ray_improve_shadows <br />
animation ray_interior_color <br />
animation_duration ray_interior_mode <br />
[[antialias]] ray_interior_reflect <br />
async_builds ray_interior_shadows <br />
[[atom_name_wildcard]] ray_interior_texture <br />
auto_classify_atoms ray_legacy_lighting <br />
auto_color ray_max_passes <br />
auto_dss [[ray_opaque_background]] <br />
auto_hide_selections [[ray_orthoscopic]] <br />
auto_indicate_flags ray_oversample_cutoff <br />
auto_number_selections ray_pixel_scale <br />
auto_remove_hydrogens [[ray_shadow]] <br />
auto_sculpt ray_shadow_decay_factor <br />
auto_show_lines ray_shadow_decay_range <br />
auto_show_nonbonded ray_shadow_fudge <br />
auto_show_selections [[ray_shadows]] <br />
auto_show_spheres ray_texture <br />
[[auto_zoom]] ray_texture_settings <br />
[[backface_cull]] ray_trace_depth_factor <br />
batch_prefix ray_trace_disco_factor <br />
[[bg_rgb]] [[ray_trace_fog]] <br />
bonding_vdw_cutoff ray_trace_fog_start <br />
button_mode [[ray_trace_frames]] <br />
button_mode_name ray_trace_gain <br />
cache_display [[Ray#Modes|ray_trace_mode]]<br />
cache_frames ray_trace_slope_factor <br />
cache_memory ray_transparency_contrast <br />
[[cartoon_color]] ray_transparency_shadows <br />
[[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br />
cartoon_debug ray_transparency_specular <br />
[[cartoon_discrete_colors]] ray_triangle_fudge <br />
[[cartoon_dumbbell_length]] [[reflect]] <br />
[[cartoon_dumbbell_radius]] reflect_power <br />
[[cartoon_dumbbell_width]] retain_order <br />
[[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br />
[[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br />
[[cartoon_flat_cycles]] ribbon_power <br />
[[cartoon_flat_sheets]] ribbon_power_b <br />
[[Cartoon_helix_radius]] ribbon_radius <br />
[[cartoon_highlight_color]] [[ribbon_sampling]] <br />
cartoon_ladder_color ribbon_side_chain_helper <br />
cartoon_ladder_mode [[ribbon_smooth]] <br />
cartoon_ladder_radius ribbon_throw <br />
cartoon_loop_cap ribbon_trace_atoms <br />
cartoon_loop_quality [[ribbon_width]] <br />
cartoon_loop_radius robust_logs <br />
[[cartoon_nucleic_acid_color]] rock_delay <br />
[[cartoon_nucleic_acid_mode]] roving_byres <br />
[[cartoon_oval_length]] roving_cartoon <br />
[[cartoon_oval_quality]] roving_delay <br />
[[cartoon_oval_width]] roving_detail <br />
cartoon_power roving_isomesh <br />
cartoon_power_b roving_isosurface <br />
cartoon_putty_quality roving_labels <br />
cartoon_putty_radius roving_lines <br />
cartoon_putty_range roving_map1_level <br />
cartoon_putty_scale_max roving_map1_name <br />
cartoon_putty_scale_min roving_map2_level <br />
cartoon_putty_scale_power roving_map2_name <br />
[[cartoon_rect_length]] roving_map3_level <br />
[[cartoon_rect_width]] roving_map3_name <br />
cartoon_refine roving_nb_spheres <br />
cartoon_refine_normals roving_nonbonded <br />
cartoon_refine_tips roving_origin <br />
cartoon_ring_color roving_origin_z <br />
cartoon_ring_finder roving_origin_z_cushion <br />
[[cartoon_ring_mode]] roving_polar_contacts <br />
cartoon_ring_radius roving_polar_cutoff <br />
[[cartoon_ring_transparency]] roving_ribbon <br />
cartoon_ring_width roving_selection <br />
[[cartoon_round_helices]] roving_spheres <br />
[[cartoon_sampling]] roving_sticks <br />
[[cartoon_side_chain_helper]] scene_animation <br />
cartoon_smooth_cycles scene_animation_duration <br />
cartoon_smooth_first scene_current_name <br />
cartoon_smooth_last scene_loop <br />
[[cartoon_smooth_loops]] scene_restart_movie_delay <br />
cartoon_throw scenes_changed <br />
cartoon_trace_atoms sculpt_angl_weight <br />
[[cartoon_transparency]] sculpt_auto_center <br />
cartoon_tube_cap sculpt_avd_excl <br />
cartoon_tube_quality sculpt_avd_gap <br />
cartoon_tube_radius sculpt_avd_range <br />
[[cavity_cull]] sculpt_avd_weight <br />
cgo_dot_radius sculpt_bond_weight <br />
cgo_dot_width sculpt_field_mask <br />
cgo_line_radius sculpt_hb_overlap <br />
cgo_line_width sculpt_hb_overlap_base <br />
cgo_ray_width_scale sculpt_line_weight <br />
cgo_sphere_quality sculpt_max_max <br />
cgo_transparency sculpt_max_min <br />
clamp_colors sculpt_max_scale <br />
connect_bonded sculpt_max_weight <br />
connect_cutoff sculpt_memory <br />
connect_mode sculpt_min_max <br />
coulomb_cutoff sculpt_min_min <br />
coulomb_dielectric sculpt_min_scale <br />
coulomb_units_factor sculpt_min_weight <br />
cull_spheres sculpt_nb_interval <br />
[[Dash_Gap]] sculpt_plan_weight <br />
[[Dash_Length]] sculpt_pyra_weight <br />
[[Dash_Radius]] sculpt_tors_tolerance <br />
[[Dash_Round_Ends]] sculpt_tors_weight <br />
dash_width sculpt_tri_max <br />
debug_pick sculpt_tri_min <br />
defer_builds_mode sculpt_tri_mode <br />
defer_updates sculpt_tri_scale <br />
[[depth_cue]] sculpt_tri_weight <br />
dihedral_label_position sculpt_vdw_scale <br />
dihedral_size sculpt_vdw_scale14 <br />
direct sculpt_vdw_vis_max <br />
dist_counter sculpt_vdw_vis_mid <br />
distance_exclusion sculpt_vdw_vis_min <br />
dot_color sculpt_vdw_vis_mode <br />
dot_density sculpt_vdw_weight <br />
dot_hydrogens sculpt_vdw_weight14 <br />
dot_lighting sculpting <br />
dot_mode sculpting_cycles <br />
dot_normals secondary_structure <br />
[[dot_radius]] security <br />
dot_solvent sel_counter<br />
[[dot_width]] selection_overlay <br />
draw_frames selection_round_points <br />
editor_auto_dihedral selection_visible_only <br />
editor_auto_origin [[selection_width]] <br />
editor_label_fragments selection_width_max <br />
fast_idle selection_width_scale <br />
fetch_path [[seq_view]] <br />
[[Field_Of_View]] seq_view_alignment <br />
fit_iterations seq_view_color <br />
fit_tolerance seq_view_discrete_by_state <br />
float_labels seq_view_fill_char <br />
[[fog]] seq_view_fill_color <br />
[[fog_start]] seq_view_format <br />
frame seq_view_label_color <br />
full_screen seq_view_label_mode <br />
gamma seq_view_label_spacing <br />
gaussian_b_adjust seq_view_label_start <br />
gaussian_b_floor [[seq_view_location]] <br />
gaussian_resolution seq_view_overlay <br />
gl_ambient seq_view_unaligned_color <br />
h_bond_cone seq_view_unaligned_mode <br />
h_bond_cutoff_center session_file <br />
h_bond_cutoff_edge session_migration <br />
h_bond_exclusion session_version_check <br />
h_bond_max_angle [[shininess]]<br />
h_bond_power_a show_alpha_checker <br />
h_bond_power_b show_progress <br />
[[half_bonds]] simplify_display_lists <br />
hash_max single_image <br />
hide_underscore_names slice_dynamic_grid <br />
idle_delay slice_dynamic_grid_resolution<br />
ignore_case slice_grid <br />
ignore_pdb_segi slice_height_map <br />
image_dots_per_inch slice_height_scale <br />
internal_feedback slice_track_camera <br />
[[Internal Gui|internal_gui]] slow_idle <br />
internal_gui_control_size smooth_color_triangle <br />
internal_gui_mode solvent_radius <br />
internal_gui_width spec_count <br />
[[internal_prompt]] spec_direct <br />
isomesh_auto_state spec_direct_power <br />
[[label_color]] spec_power <br />
[[Label_font_id]] [[spec_reflect]] <br />
[[Label_outline_color]] specular <br />
[[label_position]] specular_intensity <br />
[[label_shadow_mode]] [[sphere_color]] <br />
[[label_size]] [[sphere_mode]] <br />
legacy_mouse_zoom sphere_point_max_size <br />
legacy_vdw_radii sphere_point_size <br />
light [[sphere_quality]] <br />
light2 [[sphere_scale]] <br />
light3 sphere_solvent <br />
light4 [[sphere_transparency]] <br />
light5 spheroid_fill <br />
light6 spheroid_scale <br />
light7 spheroid_smooth <br />
light8 ss_helix_phi_exclude <br />
light9 ss_helix_phi_include <br />
[[light_count]] ss_helix_phi_target <br />
line_radius ss_helix_psi_exclude <br />
[[line_smooth]] ss_helix_psi_include <br />
line_stick_helper ss_helix_psi_target <br />
line_width ss_strand_phi_exclude <br />
log_box_selections ss_strand_phi_include <br />
log_conformations ss_strand_phi_target <br />
logging ss_strand_psi_exclude <br />
matrix_mode ss_strand_psi_include <br />
max_threads ss_strand_psi_target <br />
max_triangles state <br />
[[mesh_color]] static_singletons <br />
[[mesh_lighting]] [[stereo]]<br />
[[mesh_mode]] [[stereo_angle]]<br />
mesh_normals stereo_double_pump_mono <br />
[[mesh_quality]] [[stereo_mode]] <br />
mesh_radius stereo_shift <br />
mesh_solvent [[stick_ball]] <br />
[[mesh_type]] [[stick_ball_ratio]] <br />
[[mesh_width]] [[stick_color]]<br />
[[min_mesh_spacing]] stick_fixed_radius <br />
mouse_limit [[stick_nub]] <br />
mouse_restart_movie_delay stick_overlap <br />
mouse_scale stick_quality <br />
mouse_selection_mode stick_radius <br />
movie_delay [[stick_transparency]] <br />
movie_loop stick_valence_scale <br />
multiplex stop_on_exceptions <br />
no_idle surface_best <br />
nonbonded_size surface_carve_cutoff <br />
normal_workaround surface_carve_selection <br />
normalize_ccp4_maps surface_carve_state <br />
normalize_grd_maps surface_circumscribe <br />
normalize_o_maps surface_clear_cutoff <br />
nvidia_bugs surface_clear_selection <br />
opaque_background surface_clear_state <br />
[[orthoscopic]] surface_color <br />
overlay surface_debug <br />
overlay_lines surface_miserable <br />
pdb_conect_all surface_mode <br />
pdb_discrete_chains surface_normal <br />
pdb_echo_tags surface_optimize_subsets <br />
pdb_hetatm_sort surface_poor <br />
pdb_honor_model_number surface_proximity <br />
pdb_insertions_go_first surface_quality <br />
pdb_insure_orthogonal surface_ramp_above_mode <br />
pdb_literal_names surface_solvent <br />
pdb_no_end_record surface_trim_cutoff <br />
pdb_reformat_names_mode surface_trim_factor <br />
pdb_retain_ids surface_type <br />
pdb_standard_order suspend_updates <br />
pdb_truncate_residue_name swap_dsn6_bytes <br />
pdb_unbond_cations sweep_angle <br />
pdb_use_ter_records sweep_mode <br />
[[pickable]] sweep_phase <br />
png_file_gamma sweep_speed <br />
png_screen_gamma test1 <br />
power test2 <br />
pqr_no_chain_id text <br />
presentation texture_fonts <br />
presentation_auto_quit [[transparency]] <br />
presentation_auto_start transparency_mode <br />
presentation_mode transparency_picking_mode <br />
preserve_chempy_ids triangle_max_passes <br />
pymol_space_max_blue trim_dots <br />
pymol_space_max_green [[two_sided_lighting]]<br />
pymol_space_max_red use_display_lists <br />
pymol_space_min_factor [[valence]] <br />
raise_exceptions valence_default <br />
rank_assisted_sorts valence_size <br />
ray_blend_blue validate_object_names <br />
ray_blend_colors [[virtual_trackball]] <br />
ray_blend_green wildcard <br />
ray_blend_red wizard_prompt_mode <br />
ray_color_ramps wrap_output <br />
<br />
[[Category:Settings|All Settings]]</div>Danhttps://wiki.pymol.org/index.php?title=Virtual_trackball&diff=10617Virtual trackball2008-02-22T13:23:36Z<p>Dan: Is this better or worse?</p>
<hr />
<div>===DESCRIPTION===<br />
The '''virtual_trackbal''' setting allows you to toggle on or off the virtual trackball feature.<br />
<br />
===USAGE===<br />
set virtual_trackball, <state><br />
<br />
===PYMOL API===<br />
<source lang="python"><br />
cmd.set("virtual_trackball", <state>)<br />
</source><br />
<br />
===EXAMPLES===<br />
<source lang="python"><br />
set virtual_trackball, off<br />
set virtual_trackball, 0 #off<br />
<br />
set virtual_trackball, on<br />
set virtual_trackball, 1 #on<br />
</source> <br />
<br />
===NOTES===<br />
The virtual trackball is a less precise, more 'intuitive' way of manipulating a 3-dimensional scene.<br />
<br />
===SEE ALSO===<br />
[[Set]]<br />
<br />
[[Category:Settings|Virtual trackball]]</div>Danhttps://wiki.pymol.org/index.php?title=Virtual_trackball&diff=10616Virtual trackball2008-02-22T13:22:05Z<p>Dan: Is this better or worse?</p>
<hr />
<div>===DESCRIPTION===<br />
The '''virtual_trackbal''' setting allows you to toggle on or off the virtual trackball feature.<br />
<br />
===USAGE===<br />
set virtual_trackball, <state><br />
<br />
===PYMOL API===<br />
<source lang="python"><br />
cmd.set("virtual_trackball", <state>)<br />
</source><br />
<br />
===EXAMPLES===<br />
<source lang="python"><br />
set virtual_trackball, off<br />
set virtual_trackball, 0 #off<br />
<br />
set virtual_trackball, on<br />
set virtual_trackball, 1 #on<br />
</source> <br />
<br />
===NOTES===<br />
Other stuff<br />
<br />
===SEE ALSO===<br />
Related stuff<br />
<br />
[[Category:Settings|Virtual trackball]]</div>Danhttps://wiki.pymol.org/index.php?title=User:Dan&diff=3019User:Dan2008-02-22T13:19:00Z<p>Dan: </p>
<hr />
<div>Hi!<br />
<br />
I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].<br />
<br />
My website is [http://biodatabase.org MetaBase]<br />
<br />
<br />
<br />
== Useful links ==<br />
* [[:Category:Commands]]<br />
* [[:Category: Settings]]<br />
<br />
<br />
Template for documentation of commands / settings<br />
<pre><br />
===DESCRIPTION===<br />
'''bold name''' description<br />
<br />
===USAGE===<br />
command line usage<br />
<br />
===PYMOL API===<br />
api usage<br />
<br />
===EXAMPLES===<br />
example usage<br />
<br />
===NOTES===<br />
Other stuff<br />
<br />
===SEE ALSO===<br />
Related stuff<br />
</pre></div>Danhttps://wiki.pymol.org/index.php?title=User:Dan&diff=3018User:Dan2008-02-22T13:18:14Z<p>Dan: </p>
<hr />
<div>Hi!<br />
<br />
I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].<br />
<br />
My website is [http://biodatabase.org MetaBase]<br />
<br />
<br />
<br />
== Useful links ==<br />
* [[:Category:Commands]]<br />
<br />
<br />
<br />
<br />
===DESCRIPTION===<br />
'''bold name''' description<br />
<br />
===USAGE===<br />
command line usage<br />
<br />
===PYMOL API===<br />
api usage<br />
<br />
===EXAMPLES===<br />
example usage<br />
<br />
===NOTES===<br />
Other stuff<br />
<br />
===SEE ALSO===<br />
Related stuff</div>Danhttps://wiki.pymol.org/index.php?title=User:Dan&diff=3017User:Dan2008-02-22T13:16:28Z<p>Dan: </p>
<hr />
<div>Hi!<br />
<br />
I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].<br />
<br />
My website is [http://biodatabase.org MetaBase]<br />
<br />
<br />
<br />
<br />
===DESCRIPTION===<br />
'''bold name''' description<br />
<br />
===USAGE===<br />
command line usage<br />
<br />
===PYMOL API===<br />
api usage<br />
<br />
===EXAMPLES===<br />
example usage<br />
<br />
===NOTES===<br />
Other stuff<br />
<br />
===SEE ALSO===<br />
Related stuff</div>Danhttps://wiki.pymol.org/index.php?title=Talk:Example_Scripts&diff=319Talk:Example Scripts2008-02-21T12:52:45Z<p>Dan: New page: Where do I go for more help writing scripts? --~~~~</p>
<hr />
<div>Where do I go for more help writing scripts? --[[User:Dan|Dan]] 06:52, 21 February 2008 (CST)</div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8527Rasmolify2008-02-21T12:50:32Z<p>Dan: categorized</p>
<hr />
<div>Here it is! Long awaited, less tested;<br />
<br />
== Install ==<br />
; Linux : In your ~/.pymolrc set something like the following <PRE> run ~/pymolscripts/rasmolify.py </PRE> Finally, make a directory called ~/pymolscripts and copy the code below into a file called rasmolify.py - That should do the trick. You may also like to add a line that reads <PRE>set virtual_trackball, off</PRE> in your ~/.pymolrc<br />
<br />
; Windows : ???<br />
<br />
== Usage ==<br />
Think 'rasmol'<br />
<br />
== Code ==<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/0<br />
<br />
## TODO: <br />
<br />
## Check if a 'current' selection exists, and perform the action on<br />
## that selection. Make 'off' proper. Add units to the commands that<br />
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.<br />
<br />
## spacefill<br />
def spacefill(toggle=1):<br />
if(toggle==1):<br />
cmd.show("spheres")<br />
else:<br />
cmd.hide("spheres")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(toggle=1):<br />
if(toggle==1):<br />
cmd.show("cartoon")<br />
else:<br />
cmd.hide("cartoon")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(toggle=1):<br />
if(toggle==1):<br />
cmd.show("lines")<br />
else:<br />
cmd.hide("lines")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
<br />
</source><br />
<br />
[[Category:Script_Library]]</div>Danhttps://wiki.pymol.org/index.php?title=Rasmol&diff=9910Rasmol2008-02-21T12:11:26Z<p>Dan: </p>
<hr />
<div>The program '''rasmol''' is another molecular graphics visualization tool.<br />
<br />
For using 'rasmol-like' syntax within PyMOL, you can try [[Rasmolify]].<br />
<br />
== See also == <br />
* [[PyMOL]]</div>Danhttps://wiki.pymol.org/index.php?title=Talk:Rasmolify&diff=121Talk:Rasmolify2008-02-20T13:44:47Z<p>Dan: New page: Thanks to scripts found here; http://www.ebi.ac.uk/~gareth/pymol/ --~~~~</p>
<hr />
<div>Thanks to scripts found here; http://www.ebi.ac.uk/~gareth/pymol/ --[[User:Dan|Dan]] 07:44, 20 February 2008 (CST)</div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8526Rasmolify2008-02-20T13:43:02Z<p>Dan: /* Install */</p>
<hr />
<div>Here it is! Long awaited, less tested;<br />
<br />
== Install ==<br />
; Linux : In your ~/.pymolrc set something like the following <PRE> run ~/pymolscripts/rasmolify.py </PRE> Finally, make a directory called ~/pymolscripts and copy the code below into a file called rasmolify.py - That should do the trick. You may also like to add a line that reads <PRE>set virtual_trackball, off</PRE> in your ~/.pymolrc<br />
<br />
; Windows : ???<br />
<br />
== Usage ==<br />
Think 'rasmol'<br />
<br />
== Code ==<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/0<br />
<br />
## TODO: <br />
<br />
## Check if a 'current' selection exists, and perform the action on<br />
## that selection. Make 'off' proper. Add units to the commands that<br />
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.<br />
<br />
## spacefill<br />
def spacefill(toggle=1):<br />
if(toggle==1):<br />
cmd.show("spheres")<br />
else:<br />
cmd.hide("spheres")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(toggle=1):<br />
if(toggle==1):<br />
cmd.show("cartoon")<br />
else:<br />
cmd.hide("cartoon")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(toggle=1):<br />
if(toggle==1):<br />
cmd.show("lines")<br />
else:<br />
cmd.hide("lines")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
<br />
</source></div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8525Rasmolify2008-02-20T13:42:11Z<p>Dan: </p>
<hr />
<div>Here it is! Long awaited, less tested;<br />
<br />
== Install ==<br />
; Linux : In your ~/.pymolrc set something like the following <PRE> run ~/pymolscripts/rasmolify.py </PRE> Finally, make a directory called ~/pymolscripts and copy the code below into a file called rasmolify.py - That should do the trick. You may also like to add a line that reads <PRE>set virtual_trackball, off</PRE> in your ~/.pymolrc<br />
<br />
== Usage ==<br />
Think 'rasmol'<br />
<br />
== Code ==<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/0<br />
<br />
## TODO: <br />
<br />
## Check if a 'current' selection exists, and perform the action on<br />
## that selection. Make 'off' proper. Add units to the commands that<br />
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.<br />
<br />
## spacefill<br />
def spacefill(toggle=1):<br />
if(toggle==1):<br />
cmd.show("spheres")<br />
else:<br />
cmd.hide("spheres")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(toggle=1):<br />
if(toggle==1):<br />
cmd.show("cartoon")<br />
else:<br />
cmd.hide("cartoon")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(toggle=1):<br />
if(toggle==1):<br />
cmd.show("lines")<br />
else:<br />
cmd.hide("lines")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
<br />
</source></div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8524Rasmolify2008-02-20T13:34:53Z<p>Dan: </p>
<hr />
<div>Here it is! Long awaited, less tested;<br />
<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/0<br />
<br />
## TODO: <br />
<br />
## Check if a 'current' selection exists, and perform the action on<br />
## that selection. Make 'off' proper. Add units to the commands that<br />
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.<br />
<br />
## spacefill<br />
def spacefill(toggle=1):<br />
if(toggle==1):<br />
cmd.show("spheres")<br />
else:<br />
cmd.hide("spheres")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(toggle=1):<br />
if(toggle==1):<br />
cmd.show("cartoon")<br />
else:<br />
cmd.hide("cartoon")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(toggle=1):<br />
if(toggle==1):<br />
cmd.show("lines")<br />
else:<br />
cmd.hide("lines")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
<br />
</source></div>Danhttps://wiki.pymol.org/index.php?title=Talk:Virtual_trackball&diff=282Talk:Virtual trackball2008-02-20T13:28:54Z<p>Dan: New page: How do I do this through the API? --~~~~</p>
<hr />
<div>How do I do this through the API? --[[User:Dan|Dan]] 07:28, 20 February 2008 (CST)</div>Danhttps://wiki.pymol.org/index.php?title=Rasmolify&diff=8523Rasmolify2008-02-20T13:24:27Z<p>Dan: rasmolify your life</p>
<hr />
<div><br />
Here it is! Long awaited, less tested;<br />
<br />
<source lang="python"><br />
## This is just a quick hack. For something more meaty see;<br />
## http://arcib.dowling.edu/sbevsl/<br />
<br />
## Version 0.0.00-000/0<br />
<br />
## TODO: <br />
<br />
## Check if a 'current' selection exists, and perform the action on<br />
## that selection. Make 'off' proper. Add units to the commands that<br />
## take them.<br />
<br />
## spacefill<br />
def spacefill(toggle=1):<br />
if(toggle==1):<br />
cmd.show("spheres")<br />
else:<br />
cmd.hide("spheres")<br />
cmd.extend("spacefill", spacefill)<br />
<br />
## cartoon<br />
def cartoon(toggle=1):<br />
if(toggle==1):<br />
cmd.show("cartoon")<br />
else:<br />
cmd.hide("cartoon")<br />
cmd.extend("cartoon", cartoon)<br />
<br />
## wireframe<br />
def wireframe(toggle=1):<br />
if(toggle==1):<br />
cmd.show("lines")<br />
else:<br />
cmd.hide("lines")<br />
cmd.extend("wireframe", wireframe)<br />
<br />
<br />
## exit<br />
def exit():<br />
cmd.quit()<br />
cmd.extend("exit", exit)<br />
<br />
</source></div>Danhttps://wiki.pymol.org/index.php?title=Category_talk:Script_Library&diff=4122Category talk:Script Library2008-02-19T08:45:11Z<p>Dan: </p>
<hr />
<div>Cant you make this using a DPL? --[[User:Dan|Dan]] 10:39, 18 February 2008 (CST)<br />
<br />
About the rasmolify script, there's a project to translate between the languages [http://arcib.dowling.edu/sbevsl/].<br />
It's in pre-alpha, apparently, but this kind of language translation seems like a tricky problem. It's on my list of things to do...--[[User:Gilleain|Gilleain]] 19:27, 18 February 2008 (CST)<br />
<br />
: To be honest I was thinking of a quick hack rather than anything fancy. Thanks very much for the pointer though! --[[User:Dan|Dan]] 02:45, 19 February 2008 (CST)</div>Danhttps://wiki.pymol.org/index.php?title=Category:Script_Library&diff=3892Category:Script Library2008-02-18T16:55:57Z<p>Dan: /* Descriptions */</p>
<hr />
<div>= Overview =<br />
Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.<br />
<br />
= Descriptions =<br />
<br />
* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.<br />
<br />
* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.<br />
<br />
* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.<br />
<br />
* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.<br />
<br />
* [[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).<br />
<br />
* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)<br />
<br />
* [[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.<br />
<br />
* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.<br />
<br />
* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X<br />
<br />
* [[Show aromatics]] -- This script will display a backbone "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)<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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)<br />
<br />
* [[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. <br />
<br />
* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])<br />
<br />
* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.<br />
<br />
* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.<br />
<br />
* [[Symmetry Axis]] -- Draw a 3D-CGO line given a point and a direction. <br />
<br />
* [[CGO Text]] -- Creates a 3D-CGO text object.<br />
<br />
* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).<br />
<br />
* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).<br />
<br />
* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').<br />
<br />
* [[Split Movement]] -- Moves two parts of one object into different directions.<br />
<br />
* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.<br />
<br />
* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.<br />
<br />
* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).<br />
<br />
* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''<br />
<br />
* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''<br />
<br />
* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''<br />
<br />
* [[Measure Distance]] -- Measures the distance between two atoms (Python script).<br />
<br />
* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.<br />
<br />
* [[Color Objects]] -- Colors all objects differently (Python script).<br />
<br />
* [[Key Wait]] -- Process key events in a Python script.<br />
<br />
* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)<br />
<br />
* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)<br />
<br />
* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)<br />
<br />
* [[resicolor]] -- Colors proteins according to residue type.<br />
<br />
* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.<br />
<br />
* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!<br />
<br />
* [[grepsel]] -- Make named selections using regular expressions (protein sequence).<br />
<br />
* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.<br />
<br />
* [[Plane Wizard]] -- Wizard to draw planes between three picked points.<br />
<br />
* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.<br />
<br />
* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence<br />
<br />
* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere<br />
<br />
* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.<br />
<br />
* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.<br />
<br />
* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).<br />
<br />
[[Category:Scripting|Script Library]]</div>Danhttps://wiki.pymol.org/index.php?title=Talk:Read_PDB-String&diff=10674Talk:Read PDB-String2008-02-18T16:42:32Z<p>Dan: New page: More details here would be nice! --~~~~</p>
<hr />
<div>More details here would be nice! --[[User:Dan|Dan]] 10:42, 18 February 2008 (CST)</div>Danhttps://wiki.pymol.org/index.php?title=User:Dan&diff=3016User:Dan2008-02-18T16:41:07Z<p>Dan: Sorry for the spam ;-)</p>
<hr />
<div>Hi!<br />
<br />
I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].<br />
<br />
My website is [http://biodatabase.org MetaBase]</div>Danhttps://wiki.pymol.org/index.php?title=Category_talk:Script_Library&diff=4120Category talk:Script Library2008-02-18T16:39:38Z<p>Dan: </p>
<hr />
<div>Cant you make this using a DPL? --[[User:Dan|Dan]] 10:39, 18 February 2008 (CST)</div>Danhttps://wiki.pymol.org/index.php?title=PyMOL&diff=9869PyMOL2008-02-18T16:38:44Z<p>Dan: seems logical</p>
<hr />
<div>#REDIRECT [[Main Page]]</div>Danhttps://wiki.pymol.org/index.php?title=Rasmol&diff=9909Rasmol2008-02-18T16:38:27Z<p>Dan: looking for a 'rasmolify' script</p>
<hr />
<div>The program '''rasmol''' is another molecular graphics visualization tool.<br />
<br />
== See also == <br />
* [[PyMOL]]</div>Dan