Editing Biochemistry student intro (section)

== The "Faster" way ==
The real power of PyMOL, comes into power, when your write a PyMOL command file.<br>
Here you write which commands pymol should execute, and so it only take 1 second to get the same.<br>
The commands are stored in a ".pml" file.

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

<syntaxhighlight lang="python">
# Best to restart PyMOL every time from fresh
reinitialize
cd C:\Users\DIG\pymol

fetch 1lev, async=0
preset.publication(selection='all')
remove chain F
select substrates, organic
select f6p, resn F6P
zoom f6p
util.cbac('f6p')

select act_site, byres f6p around 3.5
show sticks, act_site

distance pol_cont, f6p, act_site, mode=2

select cli, /1lev//A/CLI # OR: select cli, resn CLI
select mn, name MN # OR: select mn, symbol Mn # OR: select mn, inorganic
show spheres, mn

label act_site and name CB, resn+resi

zoom pol_cont
viewport 1024,768
bg_color white
ray
png 1lev.png
</syntaxhighlight>

# "#" Line starting with hashes is not read by PyMOL. Use a comment field.
# Best to restart PyMOL every time from fresh
# Go to your working directory
# Get the pdb file from the RCSB server. async=0 makes sure it waits for completion of download before continuing.

Then you just open the .pml file with PyMOL. <br>
Or start PyMOL, and write in command: '''@1lev.pml''' <br>
Or start PyMOL, top menu -> File -> Run... -> C:\Users\YOU\pymol\1lev.pml

=== Movie of 1LEV ===
File: '''1lev_movie.pml'''<br>
Note, you need the '''movie.pml''' file in same directory, see [[Biochemistry_student_intro#By_a_movie_file]].
<syntaxhighlight lang="python">
fetch 1lev, async=0
preset.publication(selection='all')
remove chain F
select substrates, organic
select f6p, resn F6P
zoom f6p
util.cbac('f6p')
 
select act_site, byres f6p around 3.5
show sticks, act_site
 
distance pol_cont, f6p, act_site, mode=2
 
select cli, /1lev//A/CLI # OR: select cli, resn CLI
select mn, name MN 
# OR: select mn, symbol Mn # OR: select mn, inorganic
show spheres, mn
 
label act_site and name CB, resn+resi
 
zoom pol_cont
viewport 1024,768
bg_color white

###### Movie
# Reset
hide sticks, act_site
disable pol_cont
disable cli
hide spheres, mn
disable mn

zoom 1lev
scene F1, store, Publication

zoom substrates
scene F2, store, substrates
 
zoom f6p
scene F3, store, f6p
 
show sticks, act_site
enable pol_cont
show spheres, mn

zoom pol_cont
scene F4, store, polar contacts

@movie.pml
#ray
#png 1lev.png
</syntaxhighlight>