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

Movie Making

While PyMOL's capability to produce static images is quite powerful, there are some stories that are better told through movies, than static images alone. This little page will provide the necessary ideas, links, code and examples for making movies in PyMOL.

Terminology

Image a complex movie for a moment, a movie that has camera motions, objects moving independently or in concert with other objects, changing colors and representations. To handle camera motions PyMOL must know at all times where the camera is located and what it's pointed toward (as well as clipping planes). For objects to move around or be rotated without regard to the camera (the objects themselves rotate/translate, not just the camera) then PyMOL has to store the coordinates and matrices for these objects, too. Changing colors and representations for each object must somehow also be stored. So, as you can see this is a multidimensional problem: at each time point in your movie, PyMOL must remember positions and representations, as well as make it easy for you to transition between them (interpolation).

Despite these complexities, PyMOL tries to enable movie making for even novice users. Let's start by defining a few PyMOL concepts—states, frames and scenes.

Basic Movie Terminology

object

An object is any PyMOL-object loaded into PyMOL, like atoms, molecules, complexes, etc.

All pages regarding objects

selection

A selection is a specifically chosen set of atoms, molecules, complexes etc. in PyMOL. A selection is not an object, it's a subset of stuff from a (collection of) object(s). Selections can be named and when named have are distinguished from objects by having parentheses around their names. For example, foo would be an object and (foo) would be some selection.

All pages regarding selections

states

A state is a particular conformation (set of coordinates) for a given object. For example an NMR ensemble could contain the same molecule, but in 20 different states. PyMOL can make movies from states. States do not store representations in PyMOL (eg. cartoons vs. sticks).

See also All pages regarding states

scenes interpolation

A scene is the staged representations of objects and the orientation of the camera.

See also All pages regarding scenes

frames

A frame can be thought of as a single frame in a movie reel. A frame stores state information and scene information.

See also All pages regarding frames

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)