Before we start!
#########################################
# A quick recap
#########################################
fetch 3chb

viewing mode
L-click	: Make selection
M-click	: Center Camera
M-wheel	: z-plane-clipping
R-click	: Open menu
L-drag	: Camera rotate
M-drag	: Camera translate
R-drag	: Camera zoom

Don't forget sequence view!

orient

fetch 2chb
editing mode
L-click	: Make pick
M-click	: Center Camera
R-click	: Open menu
L-drag	: Camera rotate
M-drag	: Camera translate
R-drag	: Camera zoom
Shift_L-drag	: Object rotate
Shift_M-drag	: Object xy-translate
Shift_R-drag	: Object z-translate
as sticks
control_L-drag	: atom xy-translate
control_R-drag	: bond rotation

rein

#########################################
# Pymol Selection
#########################################

https://pymolwiki.org/index.php/Selection_Algebra

/object-name/segi-id/chain-id/resi-id/name-id
object-name and segi and chain and resi-id and name-id
            &   s.   &   c.    &   (r)i.      &   n.

rein
fetch 2chb			
remove solvent + inorganic
orient

#########################################
# Two ways to select
#########################################

molecular obj  			select /2chb			select 2chb
molecule semi (sometimes)	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
atom range			select /2chb//D/6+8/c+o		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 .. 
#########################################

object
selection
segment 	-	segi	-	s.
chain		-	chain 	- 	c.
residue number	-	resi	-	i.
residue name 	-	resn	-	r.
atom name	-	name	-	n.
subdivision	-	&
not 		-	!
or		-	|
additional	-	+

select 2chb & c. D & i. 4 & i. 7	# does not work, no i. 7 in i. 4

select 2chb & c. D & i. 4 | i. 7
select 2chb & c. D & i. 4 + i. 7	# these are eqivalent here.
select 2chb & c. D & i. 4+7		# not eqivalent

### notice no spaces around '+' as addition selection
### notice spaces around ' + ' as seperate selection	# will fail if incorrect

#########################################
# Example : view the locations for NHS-ester linkage.
#########################################

reinitialize 
fetch 2chb, type=pdb
remove ! polymer.protein
color grey50
bg_color white
orient

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

select n-terminus of chain D
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

#########################################
# Example : view the ionic and hydrogen bonding potential of the protein
#########################################

reinitialize 
fetch 2chb, type=pdb
remove ! polymer.protein
color grey50
bg_color white
orient

#select charged residues
select c. D & r. lys+arg
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

#########################################

#########################################

reinitialize 
fetch 2chb, type=pdb
util.cbc
util.cnc
bg_color white
orient

select groups		select all, 
			select none, 
			select r. HOH, 
			select hetatm, 
			select hetatm and not resn HOH
			select organic
			select hetatm & ! resn HOH

			select polymer
			select polymer.protein
			select polymer.nucleic
			select organic
			select solvent

secondary struture	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. 
		

### Why should you get to know the selection syntax?

### all functions work with the selection algebra!

showas 		as cartoon, all
show 		show sticks, sc. + n. CA + r. PRO & n. N
color 		color red, ss h
		show nb, solvent
remove		remove solvent	
		as lines, organic					
zoom		zoom bm. first organic
dist		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  	extract chainF, c. F # creates a new object of selection
delete		delete chainF 						

There are many
https://pymol.org/pymol-command-ref.html
#########################################
# Example
#########################################

reinitialize 
fetch 2chb, async=0
orient 2chb
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

extract lig-a, organic & c. D
zoom lig-a, 20


#########################################
# Examples
#########################################

reinitialize 
fetch 2chb, async=0
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
orient 
dist hbsc, organic, sc, mode=2
dist hbbb, organic, bb, mode=2
color black, hbsc
color magenta, hbbb
hide label

# run as a script
# why not try 1nqu?


###########################################################################################################################
# Exercise 1 - making some nice coiled coil structure
###########################################################################################################################
Problems and solutions

Bruce wants a pretty picture of some coiled coils
3r4a 4dzl 4dzm 4dzn 4pn8 4pn9 4pna

fetch 3r4a 4dzl 4dzm 4dzn 4pn8 4pn9 4pna

#####################################

bg_color white
as cartoon
extra_fit n. ca, 3r4a, super
set grid_mode

# This doesn’t look good because of multiple models per asymmetric unit
# This can be solved by generating the ‘biological unit’ commonly described in the pdb

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

# This is better but hasn’t fixed the problem with 4dzm, lets clean up
# This pdb may have a problem with the biological unit descriptor, we can fix this manually

split_states 4dzm 
delete 4dzm
create new, 4dzm_0001 + 4dzm_0002

# this does not look right, this is a common problem in pymol 
# all atom identifiers are identical, pymol cannot differentiate between identical atoms
# we need to change the atom identifiers
can change segment (s.)
can chainge chain (c.)
can change residue number (i.)

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

# ok lets align them
create 4dzm, newc
delete new* + 4dzm_*

enable all
set grid_mode
extra_fit n. ca, 3r4a, super
# go orthoscopic
extra_fit n. ca, 3r4a, align
extra_fit n. ca, 3r4a, cealign
extra_fit n. ca, 3r4a, align
ray