User:Inchoate

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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 BSCB@UTMB -- my old school.

-- Jason Vertrees, PhD
Jason dot Vertrees (_at-) gmail dot com

Contents

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 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

New Scenes


New movie stuff

Cool Movies

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)

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