Tutorial-5-Building.txt

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# Building with pymol                  #
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https://pymolwiki.org/index.php/Modeling_and_Editing_Structures
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# Make Peptide in Pymol (helix, sheet)
refresh editing mode, 
bond
unbond

2x peptides, fuse
[ALT] WELIKE etc
fab CHEMISTRY, ss=1
# sequence view
alter obj01, resi=str(int(resi)+6)

pick n and c termini
fuse

fab CHEMISTRY, name-helix, ss=1 
fab CHEMISTRY, name-anti, ss=2 
fab CHEMISTRY, name-para, ss=3 

Building with pymol
The builder
[ALT]ACD etc
Joining structures
Fuse


# can use on whole proteins . . .
rein
fetch 3chb, type=pdb, async=0
remove hetatm
util.cbc
split_chains 
disable 3chb_F
disable 3chb_G
disable 3chb_H
orient
select 3chb_D & i. 103 
orient sele
show sticks, sele
util.cnc
remove 3chb_D & i. 103 & n. oxt
select 3chb_D & i. 103 & n. c
select c-term, 3chb_D & i. 103 & n. c

select 3chb_E & i. 1
orient sele
show sticks, sele
select n-term, 3chb_E & i. 1 and n. n

fuse c-term, n-term

# change phi and psi - NOT THE PEPTIDE BOND!!!
now click in space > editing mode > [CTR]-right click phi or psi  > [CTR]-left click[HOLD] and drag to rotate component about bond

Clean up nomenclature i. c. s. 
alter 3chb_E & c. E, resi=str(int(resi)+103)
alter 3chb_E & c. D, chain='E'



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# Importing and Building Small Molecules
Having trouble? --> use openbabel

Builder widget

rein
Import Lewis-y from chemdraw
Clean > Scuplt

Make Lewix-y in Pymol


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# Structural Transforations

rein
fetch 2chb, async=0
remove ! polymer
split_chains
orient

# axis
rotate x, 90, 2chb_D
# vector
rotate [1,1,1],45,2chb_E

translate [0,0,20], 2chb_D

# rotations and translations are based on the camera angle
orient
rotate x, 90, 2chb_F
turn y, 90
rotate x, 90, 2chb_F

# make a dimer
orient
create obj01, 2chb, 1, 0
rotate x, 180, obj01
translate [0,0,32], obj01
color cyan, obj01
as sticks
util.cbc
util.cnc
alter obj01, segi='nseg'
extract dimer, obj01 + 2chb

delete 2chb* + obj01
sort dimer
sculpt_activate dimer, 
sculpt_iterate all, cycles=1000
sculpt_deactivate dimer
flag free, all

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rein
fetch 2chb, async=0
remove ! polymer
split_chains
orient
util.cbc 

select interE, br. 2chb_E within 5 of 2chb_D
select interH, br. 2chb_H within 5 of 2chb_D

translate [-20,20,0], 2chb_D

show surface, interE
show surface, interH
color orange, inter* & r. ALA+CYS+PHE+ILE+LEU+MET+PRO+VAL+TRP & ! n. C+CA+N+O

util.cnc
color orange, inter* & r. ALA+CYS+PHE+ILE+LEU+MET+PRO+VAL+TRP & ! n. C+CA+N+O



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# Single chained lumazine synthase
rein
fetch 1nqu, type=pdb, async=0
remove ! polymer
util.cbc
split_chains 
show sticks, sele
color grey50
util.chainbow c. A
util.chainbow c. B

as sticks
util.cnc

# select ‘N’ of i. 1 use [ALT]G, [ALT]S to make chain
or fab GSGSGSGSGSGSGSG
# use auto-sculpting
# editing [CTL] drag


flag free, all
flag fix, all and not sele
set auto_sculpt, on

set sculpting, off
set auto_sculpt, off
flag free, all



sort newmol
select ligand, c. A
flag fix, ligand
sculpt_activate newmol 
sculpt_iterate all, cycles=1000
sculpt_deactivate newmol 
flag free, all


create obj02, obj01, 0, 1
create obj03, obj01, 0, 1
create obj04, obj01, 0, 1
create obj05, obj01, 0, 1
align obj02 & c. A, 1nqu_B
align obj03 & c. A, 1nqu_C
align obj04 & c. A, 1nqu_D
align obj05 & c. A, 1nqu_E
alter obj02, resi=str(int(resi)+200)
alter obj03, resi=str(int(resi)+400)
alter obj04, resi=str(int(resi)+600)
alter obj05, resi=str(int(resi)+800)