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.

Your First Movie

Movies can be very simple, for example, animating an NMR ensemble:

# Your first movie.
fetch 1nmr
mplay

# to stop the movie when you're ready
# type 'mstop'.

What PyMOL did here was to fetch the file from the PDB and load it into an object with 20 states. Somewhere between then and issuing mplay PyMOL created 20 frames for your object and assigned one state to each frame. This created the animated effect as we scroll through the frames.

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. When you load an PDB from disk/net it is loaded into PyMOL as an object.

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. When you pick an atom (and get the default (sele) selection) or issue the ever-popular Selection command, you get a 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

Movie Panel

The movie panel is a frame indicator strip at the bottom of the screen. It shows a little icon for which frame you're currently on, and whether or not the camera has been set for that frame.

See movie_panel for more information.

What is a Movie?

Now the we have the appropriate terminology to talk about movies in PyMOL, we can discuss what a movie really is. A movie in PyMOL is a series of frames stitched together in some way so as to create the desired animation.

Movie Making Commands

This tutorial assumes you have some basic knowledge about how to use PyMOL (eg. mousing, choosing and setting your representations, etc). If you're not yet at this level, please check out the Tutorial Category of pages (most notably the beginner tutorials).

I think it's help to think of the movie as a set of frames, like in a movie reel, so let's start there. (Each command below links to the command's PyMOL wiki page, so feel free to click through for more info.)

frame

This command tells PyMOL to set the current frame to whichever you desire. To use it, just issue the command,

frame X

where X is some integer number indicating the frame you want to go to. If you issue a frame number greater than the number of frames, PyMOL sets the frame to the highest-numbered frame you have (similarly for negative numbers or numbers smaller than the minimum numbered frame).

Let's try a quick example with frame,

# create an empty 90 frame movie
mset 1 x90
# turn on the movie panel (bottom of screen)
set movie_panel, on
# goto frame one
frame 1         
# try some intermediate frames; notice the blue indicator in the movie panel         
frame 10
frame 50
frame 90
# try going beyond the end and see what PyMOL does
frame -1
frame 100
# play through the empty movie
mplay
# stop the movie
mstop

set state

Again, states are particular stored conformations of objects. Here we use PyMOL to set and get the states, and see how PyMOL mapped them to our earlier movie example.

This command has a similar idea of frame, but works a little differently. Instead of typing,

# invalid command
state 40

in PyMOL we set the state:

# how to set a state in PyMOL
set state, stateNo, objectName

# for example
# set state to 40
set state, 40

# also, get state
get state

States & Frames (optional reading)

As an example, look at the code from the "first movie":

fetch 1nmr
mplay
# issue mstop, to stop the movie

We can do a couple things now, let's try counting the number of states and frames PyMOL now knows about:

# how many frames does PyMOL know about?
count_frames

# what about states?
count_states

and now let's see how PyMOL mapped frames to states. Using the above commands and a little Python, let's see how PyMOL mapped the frames to states:

python
for x in range(1,cmd.count_frames()+1):
  cmd.frame(x)
  print "Frame => %s; and State => %s" % ( str(x), str(cmd.get('state')))
python end

which should show a 1-1 mapping of states to frames.

mset

mset is a very powerful command. This command tells PyMOL how to assign states to frames. So, now you see why it's necessary to clearly distinguish between and use the two. Let's learn how to use mset.

The syntax for mset can be a little tricky at first. I would write the syntax as:

mset stateSpec frameSpec

which assigns the states in stateSpec to the frames in frameSpec., where stateSpec is any mset-valid state specification. PyMOl supports to patterns for stateSpec. You can do simply supply a number eg

mset 1

or you can specify a range of states—like 1 through 55 as

# setting states 1 through 55
# caution: notice the space: 1 -55, not 1-55 (this is a PyMOL parser caveat)
mset 1 -55

Simple enough. Now for frameSpec' you can specify a single frame number like so or you can specify how many frames PyMOL should use to map to your specified states with the xNumber command. This will make sense with an example

# Recall: mset stateSpec frameSpec
# so we are setting STATE 1 across a span of 90 frames
mset 1 x90

# Recall: mset stateSpec frameSpec
# so we are setting states 1..120 to the next 120 frames
mset 1 -120 x120

NB: Actually the syntax is a little more complicated than this as PyMOL's mset command has the ability to remember in which frame the prior specification left the movie. So, you can sort of chain the specifications. Type help mset in PyMOL for more info or see mset.

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)