User:Inchoate: Difference between revisions
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My name is Jason Vertrees and I'm an independent consultant working with DeLano Scientific to promote PyMOL. My previous work was in theoretical biophysics and machine learning to predict properties of proteins. | |||
Also, I am the owner of the PyMOLWiki website. I started it to help the PyMOL community store and organize information regarding PyMOL. | |||
[ | If you are interested in Biophysical, Structural or Compuational Biology, check out [http://www.bscb.utmb.edu/ BSCB@UTMB] -- my old school. | ||
-- '''Jason Vertrees, PhD <br/> | |||
''Jason dot Vertrees (_at-) gmail dot com'' | |||
= My ~/.pymolrc = | = My ~/.pymolrc = | ||
Line 30: | Line 31: | ||
set ray_opaque_background,0 | set ray_opaque_background,0 | ||
set defer_builds_mode, 3 | set defer_builds_mode, 3 | ||
set async_builds, 1 | |||
</source> | |||
== To Do == | |||
* Movie->UpdateMovie | |||
* Scene->Optmize (before saving scenes; use before optimizing) | |||
* Scene->Cache (cache's surface data) | |||
* dot_solvent | |||
=== Movie Notes === | |||
<source lang="python"> | |||
# | |||
# Simple movie of independent motions | |||
# | |||
# This create an ala and a tyr. It moves the ala indepdendent | |||
# of the tyr. | |||
# | |||
# Q: Why are the orientations off? What is the equivalent | |||
# command to moving something with mouse_motions? | |||
# reinit | |||
reinitialize | |||
set matrix_mode, 1 | |||
# turns on handy scene buttons | |||
set scene_buttons, 1 | |||
# turns on the movie panel at the bottom of the sceen | |||
set movie_panel, 1 | |||
# turns on a special mouse button panel | |||
config_mouse three_button_motions | |||
# start with an empty movie, scene 1 with 90 frames | |||
mset 1 x90 | |||
# create an ala and tyr | |||
frag ala | |||
frag tyr | |||
as spheres | |||
# create our scene | |||
translate [10, 0, 0], object=ala, camera=0 | |||
orient | |||
# store the first frame | |||
frame 1 | |||
mview store, object=ala | |||
# goto the next frame | |||
frame 45 | |||
translate [-20, 0, 0], object=ala, camera=0 | |||
orient | |||
# store this frame | |||
mview store, object=ala | |||
#reinterpolate the scene | |||
mview reinterpolate, object=ala | |||
</source> | |||
New motions | |||
* Enter alone will store+reinterpolate | |||
* Shift-Enter will just store & clears the reinterpolation | |||
* CTRL-Enter will store but not reinterpolate | |||
New Scenes | |||
* setups the scenes first | |||
* then just goto the frame you want and hit enter and the current will be stored with it | |||
* or you can right-click on the movie_panel and store with scene | |||
* purge kills the matrix info for the object | |||
New movie stuff | |||
* CTRL-LEFTCLK + DRAG RIGHT = add frame/states | |||
* CTRL-LEFTCLK + DRAG LEFT = erase frame/states | |||
* Rt clk on object | |||
** Shift+Middle = drag | |||
** shift+Left = rotate | |||
= Cool Movies = | |||
* [[File:Traj_movie.mpg]] — MD Trajectory made awesome with PyMOL; 5 MB mpg file. | |||
* [[File:Long_movie_ray.mpg]] — long movie, shows dimerization, roams around the active site, 6 MB. | |||
* [[File:Motions_movie.mpg]] — a simple movie with motions. | |||
= tRNA hairball = | |||
<source lang="python"> | |||
reinit | |||
unset movie_auto_interpolate | |||
# position molecule & view | |||
fetch 1yfg, trna, async=0 | |||
orient | |||
rotate z, 60, trna | |||
python | |||
for x in range(6): | |||
n = "trna_%s" % x | |||
cmd.create( n, "trna", 1, 1) | |||
cmd.disable("trna") | |||
cmd.translate( [0, -60, 0], "trna" ) | |||
cmd.origin("trna") | |||
for x in range(6): | |||
n = "trna_%s" % x | |||
cmd.rotate( "z", 60. * x, n) | |||
cmd.show_as("cartoon", n) | |||
cmd.origin("trna") | |||
cmd.zoom() | |||
python end | |||
mset 1x360 | |||
frame 1 | |||
orient vis | |||
mview store | |||
rots = [ [0., 1., 0.], [-1.4, 1., 0], [-1.4, -1., 0.], [0., 1., 0.], [-1.4, 1., 0.], [1.4, 1., 0.] ] | |||
ang = [120,240,360] | |||
python | |||
#for f in [120,240,360]: | |||
for f in range(len(ang)): | |||
cmd.frame(ang[f]) | |||
for t in range(6): | |||
cmd.rotate(rots[t], 120, object="trna_%s" % t) | |||
python end | |||
mview interpolate, object=trna_*, power=1 | |||
python | |||
#for f in [120,240,360]: | |||
for f in range(len(ang)): | |||
cmd.frame(ang[f]) | |||
cmd.turn('y', 120) | |||
cmd.mview(action="store") | |||
python end | |||
mview interpolate, power=1 | |||
frame 1 | |||
mplay | |||
</source> | </source> | ||
= See Also = | = See Also = | ||
[[oload]], [[Cealign]], [[find_bind]], [[zero]], [[removeAlt]], [[toGroup]], [[ribbon_width]], [[antialias]], [[cartoon_fancy_helices]], [[depth_cue]], [[ray_trace_fog]], [[ray_opaque_background]], [[defer_builds_mode]], [[ray_trace_mode]]. | [[oload]], [[Cealign]], [[find_bind]], [[zero]], [[removeAlt]], [[toGroup]], [[ribbon_width]], [[antialias]], [[cartoon_fancy_helices]], [[depth_cue]], [[ray_trace_fog]], [[ray_opaque_background]], [[defer_builds_mode]], [[ray_trace_mode]]. | ||
[[User:Inchoate|Tree]] 19:08, 26 May 2009 (UTC) |
Latest revision as of 01:14, 25 February 2010
My name is Jason Vertrees and I'm an independent consultant working with DeLano Scientific to promote PyMOL. My previous work was in theoretical biophysics and machine learning to predict properties of proteins.
Also, I am the owner of the PyMOLWiki website. I started it to help the PyMOL community store and organize information regarding PyMOL.
If you are interested in Biophysical, Structural or Compuational Biology, check out BSCB@UTMB -- my old school.
-- Jason Vertrees, PhD
Jason dot Vertrees (_at-) gmail dot com
My ~/.pymolrc
run ~/playground/pymol_scripts/oload.py
run ~/playground/cealign/qkabsch.py
run ~/playground/cealign/cealign.py
run ~/playground/pymol_scripts/find_bind.py
run ~/playground/pymol_scripts/zero.py
run ~/playground/pymol_scripts/removeAlt.py
run ~/playground/pymol_scripts/toGroup.py
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
set ribbon_width, 8
set antialias,2
set cartoon_fancy_helices,1
set ray_trace_mode,1
set depth_cue,0
set ray_trace_fog,0
set ray_opaque_background,0
set defer_builds_mode, 3
set async_builds, 1
To Do
- Movie->UpdateMovie
- Scene->Optmize (before saving scenes; use before optimizing)
- Scene->Cache (cache's surface data)
- dot_solvent
Movie Notes
#
# Simple movie of independent motions
#
# This create an ala and a tyr. It moves the ala indepdendent
# of the tyr.
#
# Q: Why are the orientations off? What is the equivalent
# command to moving something with mouse_motions?
# reinit
reinitialize
set matrix_mode, 1
# turns on handy scene buttons
set scene_buttons, 1
# turns on the movie panel at the bottom of the sceen
set movie_panel, 1
# turns on a special mouse button panel
config_mouse three_button_motions
# start with an empty movie, scene 1 with 90 frames
mset 1 x90
# create an ala and tyr
frag ala
frag tyr
as spheres
# create our scene
translate [10, 0, 0], object=ala, camera=0
orient
# store the first frame
frame 1
mview store, object=ala
# goto the next frame
frame 45
translate [-20, 0, 0], object=ala, camera=0
orient
# store this frame
mview store, object=ala
#reinterpolate the scene
mview reinterpolate, object=ala
New motions
- Enter alone will store+reinterpolate
- Shift-Enter will just store & clears the reinterpolation
- CTRL-Enter will store but not reinterpolate
New Scenes
- setups the scenes first
- then just goto the frame you want and hit enter and the current will be stored with it
- or you can right-click on the movie_panel and store with scene
- purge kills the matrix info for the object
New movie stuff
- CTRL-LEFTCLK + DRAG RIGHT = add frame/states
- CTRL-LEFTCLK + DRAG LEFT = erase frame/states
- Rt clk on object
- Shift+Middle = drag
- shift+Left = rotate
Cool Movies
- File:Traj movie.mpg — MD Trajectory made awesome with PyMOL; 5 MB mpg file.
- File:Long movie ray.mpg — long movie, shows dimerization, roams around the active site, 6 MB.
- File:Motions movie.mpg — a simple movie with motions.
tRNA hairball
reinit
unset movie_auto_interpolate
# position molecule & view
fetch 1yfg, trna, async=0
orient
rotate z, 60, trna
python
for x in range(6):
n = "trna_%s" % x
cmd.create( n, "trna", 1, 1)
cmd.disable("trna")
cmd.translate( [0, -60, 0], "trna" )
cmd.origin("trna")
for x in range(6):
n = "trna_%s" % x
cmd.rotate( "z", 60. * x, n)
cmd.show_as("cartoon", n)
cmd.origin("trna")
cmd.zoom()
python end
mset 1x360
frame 1
orient vis
mview store
rots = [ [0., 1., 0.], [-1.4, 1., 0], [-1.4, -1., 0.], [0., 1., 0.], [-1.4, 1., 0.], [1.4, 1., 0.] ]
ang = [120,240,360]
python
#for f in [120,240,360]:
for f in range(len(ang)):
cmd.frame(ang[f])
for t in range(6):
cmd.rotate(rots[t], 120, object="trna_%s" % t)
python end
mview interpolate, object=trna_*, power=1
python
#for f in [120,240,360]:
for f in range(len(ang)):
cmd.frame(ang[f])
cmd.turn('y', 120)
cmd.mview(action="store")
python end
mview interpolate, power=1
frame 1
mplay
See Also
oload, Cealign, find_bind, zero, removeAlt, toGroup, ribbon_width, antialias, cartoon_fancy_helices, depth_cue, ray_trace_fog, ray_opaque_background, defer_builds_mode, ray_trace_mode.
Tree 19:08, 26 May 2009 (UTC)