PyMOL tutorial 4 : Making Movies

Expand the description for timings. - https://github.com/PyMOL-Ross
This is an introduction to movies in PyMOL
This is a rough edit from a tutorial.
Links
https://www.pymolwiki.org/index.php/M...
https://pymolwiki.org/index.php/Mview

from the start : a little intro, additional software

00:02:18 : movies with the GUI
00:08:51 : using states in the GUI
00:10:22 : using scenes in the GUI

00:13:36 : movies on the command line - mset & mview
00:19:45 : using states on the command line
00:26:06 : using 'morph' and 'create' in movies
00:31:52 : using scenes on the command line
00:37:12 : other examples from the net

Additional software

RECOMMENDED- Pymol makes BIG movie files.
This software compresses files without losing resolution
Handbrake using RF 24

##########
00:02:18 # USING THE GUI TO MAKE A MOVIE

rein
fetch 2chb, async=0
remove hydrogen
hide all
bg_color white

select lig, organic
select bb, bb.
select sc, sc. + name ca + /*//*/PRO`*/N

as cartoon, bb
show sticks, sc + lig
util.cbc
color black, lig
util.cnc
orient bb
select none

dist hbbb, org, bb, mode=2
dist hbsc, org, sc, mode=2
color grey20, hbbb
color grey80, hbsc
hide labels

Appending multiple gui camera controls that look good!

orient
Movie ~ Program ~ Camera loop ~ Nutate ~ 30deg.4sec
Movie ~ append ~ 2s

orient c. D
Movie ~ Program ~ Camera loop ~ Nutate ~ 30deg.4sec
Movie ~ append ~ 2s

orient c. D & org
Movie ~ Program ~ Camera loop ~ Nutate ~ 30deg.4sec
Movie ~ append ~ 2s
mplay

###########
00:08:51 # cycle through my NMR/MD/morph/other states!!
rein
fetch 2adt, async=0
as sticks
Movies ~ Program ~ state loop ~ Full speed
Can just 'save as movie'

I want my states to cycle while i move around the structure
Well, you can’t do that in the GUI, sorry! (at least i dont know how)

############
00:10:22 # GUI scenes # scenes are amazing!
make scenes with
Scene ~ Store ~ F?
Movie ~ Program ~ Scene loop ~ Nutate ~ 30deg.4sec
Can be a bit clunky to use but your creative skills can get around this.

###########
00:13:36 # Movies on the command line

what is mset
mset 1 x200 (x[num]) append frames at given state

if you have states too
mset 1 -200 (-[num]) move between states (while moving between frames)
mset 1 200 ([num]) moves straight to numbered state

So, you can make some fancy movies of MD simulations, NMR, morphs!

###########
what is mview

#examples
Ligand zoom
rein
fetch 1rx1, async=0
as cartoon
as sticks, organic
mset 1 x150
orient
mview store, 1
mview store, 50
orient organic
mview store, 100
mview store, 150

commands don't have to be in sequencial order.

360° rotation
rein
fetch 1rx1, async=0
as cartoon
as sticks, organic
mset 1 x180
mview store, 1
mview store, 180
turn y, 120
mview store, 60, power=1.0
turn y, 120
mview store, 120, power=1.0

############
00:19:45 # Moving through states while moving the camera

rein
load xxx.pse # load a file with states for this one.
dress structure representations appropriately for video

mview reset
orient
mset 1 x50 -500 x50
mview interpolate
mview smooth

mview store, 1
turn x, -90
mview store, 50

mview store, 150
turn x, 90
mview store, 250

mview store, 350
turn y, 90
mview store, 450
mview store, 550

##############
00:26:06 # Movies on the command line with state control and morph
'morph' - available on pymol-2.x - transitions between structures
'create' - separates and merges objects and states
have a go with morph and create, my comments below

rein
remove hydrogen
hide all
bg_color white
select lig, organic
select bb, polymer & name c+o+n+ca
select sc, sc. + name ca + /*//*/PRO`*/N
as cartoon, bb
show sticks, sc + lig
util.cbc
color black, lig
util.cnc
orient bb
dss
create pent1, reduced, 1, 1
create mono1, reduced & s. PROA, 1, 1
create mono2, reduced & s. PROB, 1, 1
create mono3, reduced & s. PROC, 1, 1
create mono4, reduced & s. PROD, 1, 1
create mono5, reduced & s. PROE, 1, 1
Move and denature
extract pent2, mono*
delete mono*
morph morphname, pent2, pent1, refinement=1, steps=100
create fullmodel, morphname, 0, 1
smooth reduced, 10, 10
create fullmodel, reduced, 0, 101

###########
00:31:52 # Movies on the command line with scenes

With scenes you can change representations during the movie
you'll need an input structure with +380 states

###########
THIS CAN ACT AS A GOOD TEMPLATE!!
mview reset
mset 1 x400 -380 x20
set scene_animation,-1
set scene_animation_duration,0
mview interpolate
mview smooth

set representation and store scenes
scene 001, store
blar blar blar
scene 002, store
etc. . . .

control the camera interacting with the frames
scene 001
mview store, 1
turn x, -120
mview store, 50, power=1.0
turn x, -120
mview store, 100, power=1.0
turn x, -120
mview store, 150
scene 002
etc. . . .

mview interpolate
mview smooth
rewind

#############
Movies and molecular transitions in powerpoint
(Sorry youtubers, this bit has some unpublished work in it)
00:37:12 # check the internet for further examples