Editing Biochemistry student intro (section)

== Movie of Epidermal Growth Factor ==
Lets make a movie of the Molecule of the month on RCSB.org.<br>
Let's take a membrane protein, [http://www.rcsb.org/pdb/explore/explore.do?structureId=1nql 1nql@rcsb], [http://pdbwiki.org/wiki/1nql pdbwiki], 
[http://www.proteopedia.org/wiki/index.php/1nql proteopedia]<br>
[http://www.rcsb.org/pdb/101/motm.do?momID=126 June 2010 Molecule of the Month by David Goodsell]

Open Notepad, and then: '''File->Save as->All files-> C:\Users\YOU\pymol\1nql.pml'''

<syntaxhighlight lang="python">
reinitialize

fetch 1nql, type=pdb1, multiplex=1,async=0

# So we get buttons for scenes
set scene_buttons, 1
viewport 1280,800
bg_color white
set fog_start, 0.60

#### Scene 1, publication ####
show_as cartoon, all
preset.publication(selection='all')

# See http://pymolwiki.org/index.php/Single-word_Selectors
extract substrates, organic
util.cbac('substrates')
select others, inorganic
select water, solvent
# See http://pymolwiki.org/index.php/Selection_Macros
# Select organic molecules
select nag, ////NAG
select bma, ////BMA
disable bma
# Hide organic
hide everything, substrates

# Save scene 1

zoom 1nql
scene F1, store, Publication

#### Scene 2, show cysteines ####
# Select sulfurs, since they play a role
select sulf_cys, resn cys and not (name O or name N or name C)
disable sulf_cys
show sticks, sulf_cys
color sulfur, sulf_cys and elem S
set_view (\
     0.351475894,    0.052040517,    0.934747040,\
    -0.784766018,   -0.528064251,    0.324480295,\
     0.510492086,   -0.847605526,   -0.144762829,\
     0.000000000,    0.000000000, -258.137542725,\
    47.065788269,  -10.656063080,    0.561561584,\
   217.718627930,  298.556427002,  -20.000000000 )
scene F2, store, Cysteines

#### Scene 3, show organis ####
show sticks, substrates
set_view (\
    -0.350075662,   -0.229279995,   -0.908223689,\
     0.627038240,    0.662946343,   -0.409051389,\
     0.695891201,   -0.712693632,   -0.088314489,\
    -0.000047103,    0.000066929, -180.624176025,\
    29.827386856,   19.096229553,   14.554395676,\
   144.383483887,  216.888458252,  -20.000000000 )
scene F3, store, substrates

#### Scene 4, polar contacts ####
select prot_cont, byres substrates around 3.5
distance subs_bond, substrates, prot_cont, mode=2
show sticks, prot_cont
set_view (\
    -0.564916074,    0.749067366,    0.346062332,\
     0.049069319,   -0.388159811,    0.920283496,\
     0.823683023,    0.536867142,    0.182521686,\
     0.000190482,   -0.000248071,  -91.693801880,\
    25.880264282,   29.162174225,   10.565655708,\
    55.450801849,  127.955612183,  -20.000000000 )
scene F4, store, polar contacts

#@movie.pml
</syntaxhighlight>
=== GUI - Scene loop ===
# Click '''Movie'''->'''Program'''->'''Scene Loop'''->'''Steady'''->'''Program'''->'''4 seconds each'''
# Click the '''Play button''' at the lover right corner. Or write '''mplay'''.
# Click '''Movie'''->'''Reset'''
# Try also the other '''Scene Loop''' method.

=== GUI - Camera loop ===
# Click '''Mouse'''->'''# Button Motions'''. In the selection menu, under '''all''', you now have a '''M''' button!.
# '''Movie'''->'''Reset'''
# Click '''F1'''
## sel. menu '''all-[M]'''->'''Store with scene F1'''
## '''Movie'''->'''Program'''->'''Camera Loop'''->'''Y-Roll'''->'''4 seconds'''
## '''Movie'''->'''Append'''->'''2 seconds'''
## Click lower right '''Full forward button''' '''->'''
# Click '''F2'''
## sel. menu '''all-[M]'''->'''Store with scene F2'''
## '''Movie'''->'''Program'''->'''Camera Loop'''->'''X-Rock'''->'''60. deg. over 4 sec.'''
## '''Movie'''->'''Append'''->'''2 seconds'''
## Click lower right '''Full forward button''' '''->'''
# Click '''F3'''
## sel. menu '''all-[M]'''->'''Store with scene F3'''
## '''Movie'''->'''Program'''->'''Camera Loop'''->'''X-Roll'''->'''4 seconds'''
## '''Movie'''->'''Append'''->'''2 seconds'''
## Click lower right '''Full forward button'''
# Click '''F4'''
## sel. menu '''all-[M]'''->'''Store with scene F4'''
## '''Movie'''->'''Append'''->'''1 seconds'''
## Click lower right '''Full forward button'''
## sel. menu '''all-[M]'''->'''Store with scene F4'''
## '''Movie'''->'''Program'''->'''Camera Loop'''->'''Nutate'''->'''30. deg. over 8 sec.'''
## '''Movie'''->'''Append'''->'''4 seconds'''
## Click lower right '''Full backward button'''
Play

=== By a movie file ===

Open Notepad, and then: '''File->Save as->All files-> C:\Users\YOU\pymol\movie.pml'''

<syntaxhighlight lang="python">
set movie_panel, 1
mset 1 x1000

scene F1
python

f=1
cmd.frame(f)
cmd.mview("store",scene="F1")
f=f+99; print f
cmd.frame(f)
cmd.mview("store",scene="F1")

f=f+49; print f
cmd.frame(f)
cmd.mview("store",scene="F2")
f=f+99; print f
cmd.frame(f)
cmd.mview("store",scene="F2")

f=f+49; print f
cmd.frame(f)
cmd.mview("store",scene="F3")
f=f+99; print f
cmd.frame(f)
cmd.mview("store",scene="F3")

f=f+49; print f
cmd.frame(f)
cmd.mview("store",scene="F4")
f=f+99; print f
cmd.frame(f)
cmd.mview("store",scene="F4")

f=f+49; print f
cmd.frame(f)
cmd.turn('y',50)
cmd.mview("store")

f=f+99; print f
cmd.frame(f)
cmd.turn('y',-100)
cmd.mview("store")

f=f+49; print f
cmd.frame(f)
cmd.turn('y',50)
cmd.mview("store")

f=f+49; print f
cmd.frame(f)
cmd.mview("store",scene="F4")

python end

frame 1
mplay
</syntaxhighlight>
Write in pymol: '''@movie.pml'''