Revision as of 22:24, 12 June 2009

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

Imagine 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).

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.

mview

The mview command can be intimidating, but all we need to know about it at present is that it can store the (1) camera position or (2) a given object position. The idea is to essentially make 'way points' in your movie and have PyMOL interpolate the in-between positions/coordinates, etc. For example, if I wanted to make a 100-frame movie of a zoom into an object, I could store and manually set 100 camera positions, or I could do the starting position and the final position and ask PyMOL to just interpolate that over 100 frames. The latter idea is obviously much simpler. So simple in fact, let's make a super-quick movie that does exactly what I just mentioned—100 frames of a slow zoom into some object. Start with a fresh PyMOL session (reinitialize) and then copy/paste the following:

 1 # let's initialize the movie to 100 frames, all of state 1
 2 # it's ONLY state 1, because we're only moving the camera around, not
 3 # changing structure coordinates of the leucine:
 4 mset 1 x100
 5 
 6 # show a leucine
 7 frag leu
 8 
 9 # position the residue
10 orient
11 
12 # let's store the current camera position
13 mview store
14 
15 # now set our way point to be frame 100
16 frame 100
17 
18 # now let's zoom into some atom on the fragment
19 zoom ID 10
20 
21 # now save this view at frame 100
22 mview store
23 
24 # last thing is to tell PyMOL to interpolate the 100 frame zoom
25 # so we don't have to do those 100 snapshots:
26 mview reinterpolate
27 
28 # voila, you have a movie.  To watch it go back to frame 1 and play it
29 frame 1
30 mplay
31 
32 # mstop when you're ready

'But, hold on!' you might say. Why is it so herky-jerky? We have smooth zooming but then a snap and back to frame one! Well, we never gave PyMOL any number of frames to interpolate the change from frame 100 back to frame 1 (since it wraps). If we wanted an a zoom in that was equally as fast as the zoom out we would simply replace line #16 with

# now set our way point to be frame 100
frame 100

but, if we wanted a slow, zoom in and a fast zoom out we could do

# now set our way point to be frame 100
frame 80

instead which would only give PyMOL 20 frames with which to zoom us out. Try it!

Very Basic Mview Syntax

This is a simple overview, see mview for complete details.

Using mview as you can see from above is pretty simple. The very basic syntax is:

# store the camera OR some object given by objName (if it's supplied)
mview store[, object=objName]

# reinterpolate (link together the positions) for the saved camera or object
mview reinterpolate[, object=objName]

If you leave off the object=objName then you're storing the camera information only—and so none of your objects will be moving anywhere—just the camera. If you include an object name, then it stores that object's position information in the current frame. The mview store tells PyMOL to store the camera or objects coordinates, while the mview reinterpolate command tells PyMOL to link together the saved positions for the camera or the selected object in a smooth, cool way.

Simple Movie Examples

We now the ability to make some pretty simple, but cool movies. So, let's try a few.

Multiple Zooming

Let's try making a movie where we zoom into each ligand that's not water. In order to make this movie, I had to find a protein with suitable ligands, so you can do the same for your own protein. Just replace the hard-coded residue numbers.

Goal: Make a movie that zoom into the three ligands, stays on that ligand for 2 seconds, then moves to the next. I also want smooth zoom out at the end. Don't let the length of this movie script throw you off, you've seen all of the movie commands and the initial commands are just loading the and making it look good.

# setup PyMOL for the movie
reinitialize
set matrix_mode, 1
set movie_panel, 1

# load the PDB, make selections for the ligands and
# make the protein look snazzy.
#load /spc/pdb/2jep.pdb
fetch 2jep, asyn=0
remove resn HOH
orient
select l1, c. A and i. 1397
select l2, c. A and i. 1396
select l3, c. B and i. 1396
as cartoon
color grey
show sticks, het
color magnesium, het

# At 30 FPS this is then a 16 second movie.
# We look at the structure for 2 seconds, zoom in to each ligand
# and look at it for another 2 seconds, then, zoom out and look again
# at everything for another 2 seconds.

# initialize the 480 frame movie
mset 1 x480

# zoom all ('scene #1')
frame 1
mview store
# stay here for 2 seconds
frame 60
mview store

# zoom on ligand 1  ('scene #2')
frame 120
zoom l1
mview store
# stay here for 2 seconds
frame 180
mview store

# zoom on ligand 2  ('scene #3')
frame 240
zoom l2
mview store
# stay for 2 seconds
frame 300
mview store

# zoom to ligand 3  ('scene #4')
frame 360
zoom l3
mview store
# stay for 2 seconds
frame 420
mview store

# zoom out  ('back to scene #1')
frame 480
zoom
mview store

# interpolate the frames
mview reinterpolate

# play the awesome movie!
mplay

# stop when you want
# mstop

Animating an Alignment

# setup PyMOL for the movie
reinitialize
set matrix_mode, 1
set movie_panel, 1

# load the PDBs
fetch 1cll 1ggz, async=0

# orient the scene
as cartoon
orient

# make 100-frame movie
mset 1 x100
# goto frame 1
frame 1

# store the camera position and object
# positions in frame 1
mview store
mview store, object=1cll
mview store, object=1ggz

# goto frame 90
frame 90
# align the two proteins
super 1cll, 1ggz
# we rezoom to center the camera on the 
# two aligned proteins
zoom
# store the camera positions
mview store
# store the new object position(s)
mview store, object=1cll
mview store, object=1ggz

# have PyMOL stitch together the scenes.
mview reinterpolate
mview reinterpolate, object=1cll
mview reinterpolate, object=1ggz

# rewind
frame 1
# get some popcorn!  :-)
mplay

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