User:Inchoate

My name is Jason Vertrees and I'm a postdoc in computational biology. Currently, I study proteins through mathematical models & machine learning. My previous work was in theoretical biophysics.

Also, I am the owner and of the PyMOLWiki website.

If you are interested in Biophysical, Structural or Compuational Biology, check out BSCB@UTMB -- my old school.

Jason Vertrees, PhD

jv(_at-)cs_dot_dartmouth(dot2)edu

My Page

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

To Do

• texture_fonts, 1 -- for speed
• pseudo-atoms; you can label them. RightClick->New->PAtom->and then label it; move the atom (and the label goes w/it). You can also move the label by itself
• movie_panel
• mset - clears the movie
• Movie->UpdateMovie
• Scene->Buttons (shows buttons for each scene)
• Scene->Optmize (before saving scenes; use before optimizing)
• Scene->Cache (cache's surface data)
• A good way to make movies seems to be:
  • madd
  • prepare a scene; turn on scene buttons
  • Fn+CTRL+down-arrow # adds the scene;
  • madd 1 x90
  • mview store, -1
• repeat
• when done do mview reinterpolate
• play the movie
• matrix_mode
• 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

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)