User:Inchoate

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)