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 ~/.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
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)