PyMOL tutorial 2 : Making selections and using commands

Expand the description for timings. - https://github.com/PyMOL-Ross
This is an introduction to making atomic selections and using commands in PyMOL
This is a rough edit from a tutorial.
Links
https://pymolwiki.org/index.php/Selection_Algebra
https://pymol.org/pymol-command-ref.html

from the start - recap on orientation
00:05:40 - selection algebra (fundamentals)
00:17:30 - EXAMPLE: selecting primary amines for chemical linkage
00:22:08 - EXAMPLE: view charged residues and hydrogen bond acceptors/donors
00:24:15 - selection algebra (groups)
00:31:37 - examples of commands
00:37:45 - EXAMPLES: highlight sequence and measure, show h-bonds
00:42:57 - PROBLEM: generate nice picture of aligned structures
00:53:15 - QUESTION: metal ion interactions

######
00:05:40# Pymol Selection
rein
fetch 2chb
orient

###
# Two ways to select
object select /2chb select 2chb
segment select /2chb/A select 2chb & segi A
chain select /2chb//D select 2chb and chain D
residue select /2chb//D/PRO select 2chb & c. D & i. 10
residue select /2chb//D/PRO`53 select 2chb & c. D & i. 53 & r. PRO
atom select /2chb//D/10/ca select 2chb & c. D & i. 10 & n. ca
atom select ////PRO/ca select r. PRO & n. ca
atom range select /2chb//D/10-12/ca select 2chb & c. D & i. 10-12 & n. ca

select 2chb and chain D and resi 10+12 and not name ca
select 2chb & c. D & i. 10+12 & ! n. n+o+c

######
# Explained
segment - segi - s.
chain - chain - c.
residue number - resi - i.
residue name - resn - r.
atom name - name - n.
subdivision - &
not - !
additional - +

select 2chb & c. D & i. 4 + i. 7
select 2chb & c. D & i. 4+7 # not equivalent
# notice no spaces around '+' as addition selection
# notice spaces around ' + ' as separate selection

######
00:17:30 # Example : NHS-ester linkage locations
reinitialize
fetch 2chb, type=pdb
remove ! polymer
color grey50
bg_color white
orient

select lysines, c. D & r. lys
show sticks, lysines
show sphere, lysines & n. NZ
color blue, lysines & n. NZ

select nres, br. first c. D & n. N
show sticks, nres
show sphere, nres & n. N
color blue, nres & n. N

show surface
set transparency, 0.2

######
00:22:08 # Example : charged and hydrogen bonding residues
reinitialize
fetch 2chb
remove ! polymer
color grey50
bg_color white
orient

#select charged residues
show sticks, c. D & r. lys+arg+asp+glu
color grey50
color blue, c. D & r. lys+arg & ! n. c+ca+n+o+cb+cg+cd
color red, c. D & r. asp+glu & ! n. c+ca+n+o+cb+cg
show surface
set transparency, 0.2

#select hydrogen bond acceptors/doners
color grey50
color cyan, don. & c. D
color magenta, acc. & c. D

######
00:24:15 # group selections
reinitialize
fetch 2chb
util.cbc
util.cnc
bg_color white
orient

groups
select all,
select none,
select r. HOH,
select hetatm,
select hetatm & ! resn HOH
select polymer
select polymer.protein
select polymer.nucleic
select organic
select solvent

secondary structure ss (ss h+s+l(loop))
select ss h
select ss s
select polymer.protein & ! ss h+s # selects loop sections

amino acid sequence
select c. D & pepseq TEAK
select c. D & ps. TEAK

protein
select sc.
select bb.
select don.
select acc.

expand selection
byobject
bysegi bs.
bymolecule bm.
bychain bc.
byresidue br.

#####
00:31:37# all commands work with selection algebra!
as cartoon, all
show sticks, sc. + n. CA + r. PRO & n. N
show nb, solvent
color red, ss h
remove solvent
as lines, organic
zoom bm. first organic
dist temp, c. D & i. 4 & n. CA, c. E & i. 4 & n. CA
dist temp, c. D & i. 4, c. E & i. 4
extract chainF, c. F # creates new object
delete chainF

#####
00:37:45 # Example1
reinitialize
fetch 2chb, async=0
remove solvent + inorganic
color grey80, all
color firebrick, ss h
show sticks, c. D & ps. TEAK
color black, c. D & ps. TEAK
bg_color white
zoom c. D & ps. TEAK, 5
util.cnc
dist dist01, /2chb/A/D/VAL`82/CA, /2chb/A/D/ALA`75/CA
color magenta, dist01

#####
# Example2
reinitialize
fetch 2chb, async=0
orient
remove solvent + inorganic
select bb, bb.
select sc, sc. + n. CA + PRO/N
util.cbc
as cartoon, bb
show sticks, sc
color grey50, organic
util.cnc
bg_color white
dist hbsc, organic, sc, mode=2
dist hbbb, organic, bb, mode=2
color black, hbsc
color magenta, hbbb
hide label

#####
00:42:57 # Exercise 1 - making some nice coiled coil structure
rein
fetch 3r4a 4dzl 4dzm 4dzn 4pn8 4pn9 4pna, type=pdb1, async=0
bg_color white
as cartoon
extra_fit n. ca, 3r4a, super
set grid_mode

# there is a problem with 4dzm
split_states 4dzm
delete 4dzm
create new, 4dzm_0001 + 4dzm_0002

# we broke it! lets fix it
delete new
alter 4dzm_0002, segi="new0"
create news, 4dzm_0001 + 4dzm_0002
alter 4dzm_0002, chain="B"
create newc, 4dzm_0001 + 4dzm_0002
alter 4dzm_0002, resi=str(int(resi)+100)
create newi, 4dzm_0001 + 4dzm_0002

# align them
create 4dzm, newc
delete new* + 4dzm_*
extra_fit n. ca, 3r4a, align
ray

#####
00:53:15 - QUESTION: metal ion interactions
dist distname, inorganic, protein, mode=2