PyMOL Wiki - User contributions [en]

User:Dan

2008-11-28T22:31:45Z

Dan:

Hi!

I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].

My website is [http://metadatabase.org MetaBase]

== Useful links ==
* [[:Category:Commands]]
* [[:Category: Settings]]

Template for documentation of commands / settings
<pre>
===DESCRIPTION===
'''bold name''' description

===USAGE===
command line usage

===PYMOL API===
api usage

===EXAMPLES===
example usage

===NOTES===
Other stuff

===SEE ALSO===
Related stuff
</pre>

Rasmolify

2008-02-22T13:51:14Z

Dan:

Here it is! Long awaited, less tested;

== Install ==
; 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

; Windows : ???

== Usage ==
Think 'rasmol'

== Related ==
* http://arcib.dowling.edu/sbevsl/

== TODO ==
* 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).
* Implement 'scaling' units for display functions
* Fix the mouse behaviour?
* Add a rasmol GUI!

== Code ==
<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/1

## Turn off the virtual_trackball
cmd.set("virtual_trackball", "off")

## spacefill
def spacefill(p1=''):
if(p1=='off'):
cmd.hide("spheres")
elif(p1==''):
cmd.show("spheres")
else:
print("feh!")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(p1=''):
if(p1=='off'):
cmd.hide("cartoon")
elif(p1==''):
cmd.show("cartoon")
else:
print("feh!")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(p1=''):
if(p1=='off'):
cmd.hide("lines")
elif(p1==''):
cmd.show("lines")
else:
print("feh!")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)
</source>

[[Category:Script_Library]]

Rasmolify

2008-02-22T13:49:37Z

Dan:

Here it is! Long awaited, less tested;

== Install ==
; 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

; Windows : ???

== Usage ==
Think 'rasmol'

== Related ==
* http://arcib.dowling.edu/sbevsl/

== TODO ==
* Implement 'scaling' units for display functions
* Fix the mouse behaviour?
* Add a rasmol GUI!

== Code ==
<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/1

## Turn off the virtual_trackball
cmd.set("virtual_trackball", "off")

## spacefill
def spacefill(p1=''):
if(p1=='off'):
cmd.hide("spheres")
elif(p1==''):
cmd.show("spheres")
else:
print("feh!")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(p1=''):
if(p1=='off'):
cmd.hide("cartoon")
elif(p1==''):
cmd.show("cartoon")
else:
print("feh!")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(p1=''):
if(p1=='off'):
cmd.hide("lines")
elif(p1==''):
cmd.show("lines")
else:
print("feh!")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)
</source>

[[Category:Script_Library]]

Rasmolify

2008-02-22T13:47:48Z

Dan:

Here it is! Long awaited, less tested;

== Install ==
; 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

; Windows : ???

== Usage ==
Think 'rasmol'

== Code ==
<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/1

## Turn off the virtual_trackball
cmd.set("virtual_trackball", "off")

## spacefill
def spacefill(p1=''):
if(p1=='off'):
cmd.hide("spheres")
elif(p1==''):
cmd.show("spheres")
else:
print("feh!")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(p1=''):
if(p1=='off'):
cmd.hide("cartoon")
elif(p1==''):
cmd.show("cartoon")
else:
print("feh!")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(p1=''):
if(p1=='off'):
cmd.hide("lines")
elif(p1==''):
cmd.show("lines")
else:
print("feh!")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)
</source>

[[Category:Script_Library]]

Category:Settings

2008-02-22T13:25:38Z

Dan:

== Introduction ==
PyMol has over 500 settings! Everything from ray tracing fog, to perspective viewing, stereo rendering, colors, textures, memory settings and '''many''' more!

One of the most powerful features is the amount of detail and control PyMOL offers through these various settings.

For more information see [[Settings]].

Settings

2008-02-22T13:25:11Z

Dan: made a link a bit more explicit

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]]

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

[[Category:Settings|All Settings]]

Virtual trackball

2008-02-22T13:23:36Z

Dan: Is this better or worse?

===DESCRIPTION===
The '''virtual_trackbal''' setting allows you to toggle on or off the virtual trackball feature.

===USAGE===
set virtual_trackball, <state>

===PYMOL API===
<source lang="python">
cmd.set("virtual_trackball", <state>)
</source>

===EXAMPLES===
<source lang="python">
set virtual_trackball, off
set virtual_trackball, 0 #off

set virtual_trackball, on
set virtual_trackball, 1 #on
</source>

===NOTES===
The virtual trackball is a less precise, more 'intuitive' way of manipulating a 3-dimensional scene.

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

[[Category:Settings|Virtual trackball]]

Virtual trackball

2008-02-22T13:22:05Z

Dan: Is this better or worse?

===DESCRIPTION===
The '''virtual_trackbal''' setting allows you to toggle on or off the virtual trackball feature.

===USAGE===
set virtual_trackball, <state>

===PYMOL API===
<source lang="python">
cmd.set("virtual_trackball", <state>)
</source>

===EXAMPLES===
<source lang="python">
set virtual_trackball, off
set virtual_trackball, 0 #off

set virtual_trackball, on
set virtual_trackball, 1 #on
</source>

===NOTES===
Other stuff

===SEE ALSO===
Related stuff

[[Category:Settings|Virtual trackball]]

User:Dan

2008-02-22T13:19:00Z

Dan:

Hi!

I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].

My website is [http://biodatabase.org MetaBase]

== Useful links ==
* [[:Category:Commands]]
* [[:Category: Settings]]

Template for documentation of commands / settings
<pre>
===DESCRIPTION===
'''bold name''' description

===USAGE===
command line usage

===PYMOL API===
api usage

===EXAMPLES===
example usage

===NOTES===
Other stuff

===SEE ALSO===
Related stuff
</pre>

User:Dan

2008-02-22T13:18:14Z

Dan:

Hi!

I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].

My website is [http://biodatabase.org MetaBase]

== Useful links ==
* [[:Category:Commands]]

===DESCRIPTION===
'''bold name''' description

===USAGE===
command line usage

===PYMOL API===
api usage

===EXAMPLES===
example usage

===NOTES===
Other stuff

===SEE ALSO===
Related stuff

User:Dan

2008-02-22T13:16:28Z

Dan:

Hi!

I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].

My website is [http://biodatabase.org MetaBase]

===DESCRIPTION===
'''bold name''' description

===USAGE===
command line usage

===PYMOL API===
api usage

===EXAMPLES===
example usage

===NOTES===
Other stuff

===SEE ALSO===
Related stuff

Talk:Example Scripts

2008-02-21T12:52:45Z

Dan: New page: Where do I go for more help writing scripts? --~~~~

Where do I go for more help writing scripts? --[[User:Dan|Dan]] 06:52, 21 February 2008 (CST)

Rasmolify

2008-02-21T12:50:32Z

Dan: categorized

Here it is! Long awaited, less tested;

== Install ==
; 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

; Windows : ???

== Usage ==
Think 'rasmol'

== Code ==
<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/0

## TODO:

## Check if a 'current' selection exists, and perform the action on
## that selection. Make 'off' proper. Add units to the commands that
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.

## spacefill
def spacefill(toggle=1):
if(toggle==1):
cmd.show("spheres")
else:
cmd.hide("spheres")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(toggle=1):
if(toggle==1):
cmd.show("cartoon")
else:
cmd.hide("cartoon")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(toggle=1):
if(toggle==1):
cmd.show("lines")
else:
cmd.hide("lines")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)

</source>

[[Category:Script_Library]]

Rasmol

2008-02-21T12:11:26Z

Dan:

The program '''rasmol''' is another molecular graphics visualization tool.

For using 'rasmol-like' syntax within PyMOL, you can try [[Rasmolify]].

== See also ==
* [[PyMOL]]

Talk:Rasmolify

2008-02-20T13:44:47Z

Dan: New page: Thanks to scripts found here; http://www.ebi.ac.uk/~gareth/pymol/ --~~~~

Thanks to scripts found here; http://www.ebi.ac.uk/~gareth/pymol/ --[[User:Dan|Dan]] 07:44, 20 February 2008 (CST)

Rasmolify

2008-02-20T13:43:02Z

Dan: /* Install */

Here it is! Long awaited, less tested;

== Install ==
; 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

; Windows : ???

== Usage ==
Think 'rasmol'

== Code ==
<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/0

## TODO:

## Check if a 'current' selection exists, and perform the action on
## that selection. Make 'off' proper. Add units to the commands that
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.

## spacefill
def spacefill(toggle=1):
if(toggle==1):
cmd.show("spheres")
else:
cmd.hide("spheres")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(toggle=1):
if(toggle==1):
cmd.show("cartoon")
else:
cmd.hide("cartoon")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(toggle=1):
if(toggle==1):
cmd.show("lines")
else:
cmd.hide("lines")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)

</source>

Rasmolify

2008-02-20T13:42:11Z

Dan:

Here it is! Long awaited, less tested;

== Install ==
; 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

== Usage ==
Think 'rasmol'

== Code ==
<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/0

## TODO:

## Check if a 'current' selection exists, and perform the action on
## that selection. Make 'off' proper. Add units to the commands that
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.

## spacefill
def spacefill(toggle=1):
if(toggle==1):
cmd.show("spheres")
else:
cmd.hide("spheres")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(toggle=1):
if(toggle==1):
cmd.show("cartoon")
else:
cmd.hide("cartoon")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(toggle=1):
if(toggle==1):
cmd.show("lines")
else:
cmd.hide("lines")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)

</source>

Rasmolify

2008-02-20T13:34:53Z

Dan:

Here it is! Long awaited, less tested;

<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/0

## TODO:

## Check if a 'current' selection exists, and perform the action on
## that selection. Make 'off' proper. Add units to the commands that
## take them. Turn off the virtual_trackball. Fix the mouse behaviour.

## spacefill
def spacefill(toggle=1):
if(toggle==1):
cmd.show("spheres")
else:
cmd.hide("spheres")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(toggle=1):
if(toggle==1):
cmd.show("cartoon")
else:
cmd.hide("cartoon")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(toggle=1):
if(toggle==1):
cmd.show("lines")
else:
cmd.hide("lines")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)

</source>

Talk:Virtual trackball

2008-02-20T13:28:54Z

Dan: New page: How do I do this through the API? --~~~~

How do I do this through the API? --[[User:Dan|Dan]] 07:28, 20 February 2008 (CST)

Rasmolify

2008-02-20T13:24:27Z

Dan: rasmolify your life

Here it is! Long awaited, less tested;

<source lang="python">
## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/0

## TODO:

## Check if a 'current' selection exists, and perform the action on
## that selection. Make 'off' proper. Add units to the commands that
## take them.

## spacefill
def spacefill(toggle=1):
if(toggle==1):
cmd.show("spheres")
else:
cmd.hide("spheres")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(toggle=1):
if(toggle==1):
cmd.show("cartoon")
else:
cmd.hide("cartoon")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(toggle=1):
if(toggle==1):
cmd.show("lines")
else:
cmd.hide("lines")
cmd.extend("wireframe", wireframe)

## exit
def exit():
cmd.quit()
cmd.extend("exit", exit)

</source>

Category talk:Script Library

2008-02-19T08:45:11Z

Dan:

Cant you make this using a DPL? --[[User:Dan|Dan]] 10:39, 18 February 2008 (CST)

About the rasmolify script, there's a project to translate between the languages [http://arcib.dowling.edu/sbevsl/].
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)

: 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)

Category:Script Library

2008-02-18T16:55:57Z

Dan: /* Descriptions */

= Overview =
Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.

= Descriptions =

* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.

* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.

* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.

* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.

* [[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.

* [[Symmetry Axis]] -- Draw a 3D-CGO line given a point and a direction.

* [[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''

* [[apropos]] -- List all commands matching a given keyword or whose docs contain the 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)

* [[resicolor]] -- Colors proteins according to residue type.

* [[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.

* [[Plane Wizard]] -- Wizard to draw planes between three picked points.

* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.

* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence

* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere

* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.

* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.

* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).

[[Category:Scripting|Script Library]]

Talk:Read PDB-String

2008-02-18T16:42:32Z

Dan: New page: More details here would be nice! --~~~~

More details here would be nice! --[[User:Dan|Dan]] 10:42, 18 February 2008 (CST)

User:Dan

2008-02-18T16:41:07Z

Dan: Sorry for the spam ;-)

Hi!

I sometimes use [[PyMOL]], but to be honest I prefer [[Rasmol]].

My website is [http://biodatabase.org MetaBase]

Category talk:Script Library

2008-02-18T16:39:38Z

Dan:

Cant you make this using a DPL? --[[User:Dan|Dan]] 10:39, 18 February 2008 (CST)

PyMOL

2008-02-18T16:38:44Z

Dan: seems logical

#REDIRECT [[Main Page]]

Rasmol

2008-02-18T16:38:27Z

Dan: looking for a 'rasmolify' script

The program '''rasmol''' is another molecular graphics visualization tool.

== See also ==
* [[PyMOL]]