PyMOL tutorial 5 : Building and Manipulating

Expand the description for timings. - https://github.com/PyMOL-Ross
This is an introduction to building molecules PyMOL
This is a rough edit from a tutorial.
Links
https://pymolwiki.org/index.php/Model...

Timings
From the beginning - Intro
00:00:48 - Making peptides
00:06:35 - Joining protein domains
00:09:11 - Building and importing small molecules
00:12:54 - Transformations (rotate and translate)
00:15:58 - Generate a dimer
00:17:46 - Show intra-oligomer interface
00:18:33 - Single chained lumazine synthase

########################################
00:00:48 # Make Peptide in Pymol (helix, sheet)

Hold [ALT] then type peptide sequence 'WELIKE'

fab CHEMISTRY, ss=1

check sequence view, make identifiers unique
alter obj01, resi=str(int(resi)+6)

pick n and c termini
fuse

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

Check out the building widget

########################################
00:06:35 # 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 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

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

########################################
00:09:11 # Importing and Building Small Molecules
Having trouble? -- use openbabel

Builder widget

rein
Import Lewis-y from chemdraw
Clean ~ Scuplt

########################################
00:12:54 # Structural Transformations

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
unless
rotate x, 90, 2chb_D, camera=0

########################################
00:15:58 # 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

########################################
00:17:46 # show intra-oligomer interface

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

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

########################################
00:18:33 # 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)