PyMOL Quickie - Making Mutations

MAKING MUTATIONS - https://github.com/PyMOL-Ross

00:00:24 Introduction - mutations and amino acids
00:04:11 Introduction - rotamers and states
00:06:26 GUI - making mutations
00:12:41 GUI - remove clashes with sculpting
00:15:17 Command line - making mutations
00:17:55 Command line - remove clashes with sculpting
00:22:03 BASH scripting

to run the bash commands, replace '(out into)' below, with the right-hand facing arrow key (which are not allowed in the comments!)


MUTATIONS USING THE GUI
00:06:26
rein
load molecule
Crystal Structure of heterodimeric L. donovani topoisomerase I
fetch 2B9S

clean and present
remove ! polymer
util.cbc
show sticks, sc. + n. CA + r. PRO & n. N
as sticks, polymer.nucleic
bg_color white
util.cnc
orient

#### Make mutation
Wizard :: Mutagenesis :: Protein

Find and pick your residue
can also use sequence view
states unmutated
use state controls to cycle through rotamers
pick new residue
[No Mutation] button has choices
states mutated
use state controls to cycle through rotamers

00:12:41 # then
Build :: Sculpting :: Sculpting
Build :: Sculpting :: Activate

allow to relax
Build :: Sculpting :: Deactivate
Build :: Sculpting :: Sculpting

also
Wizard :: Mutagenesis :: nucleic acids

00:15:17
MUTATIONS USING THE COMMAND LINE
rein

load molecule
Crystal Structure of heterodimeric L. donovani topoisomerase I
fetch 2B9S

clean and present
remove ! polymer
util.cbc
show sticks, sc. + n. CA + r. PRO & n. N
as sticks, polymer.nucleic
bg_color white
util.cnc
orient

Turn on the wizard
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")

mutate chain A residue 352 to PHE
cmd.get_wizard().set_mode("HIS")
cmd.get_wizard().do_select("A/150/")

Apply mutation
cmd.get_wizard().apply()

00:17:55
relax structure
select mutant, A/150/
select new, br. mutant gap 10
flag fix, br. mutant gap 10
sculpt_activate 2B9S
sculpt_iterate all, cycles=2000
sculpt_deactivate 2B9S


00:22:03
MUTATIONS USING A BASH SCRIPT
prepare you input file in pymol
select br. polymer.protein within 5 of polymer.nucleic
save interact.pdb, sele

prepare you input file in bash
grep ' CA ' interact.pdb | cut -c 22-27 | sed 's/ /\//g;s/\/\//\//g' (out into) res.list

This is the BASH script

for YYY in $(cat res.list | head -5) ; do
for XXX in ALA LYS ; do

chain=$(echo $YYY | cut -c 1)
num=$(echo $YYY | cut c 3 | rev | cut c 2 | rev)

echo -en "\rmutating chain $chain res $num to $XXX"

echo "
rein
fetch 2B9S, async=0
remove ! polymer

cmd.wizard(\"mutagenesis\")
cmd.do(\"refresh_wizard\")

lets mutate residue 104 to GLN
cmd.get_wizard().set_mode(\"$XXX\")
cmd.get_wizard().do_select(\"$YYY\")

Apply the mutation
cmd.get_wizard().apply()
cmd.get_wizard().done()

select mutant, $YYY
flag fix, br. mutant gap 10
sculpt_activate 2B9S
sculpt_iterate all, cycles=1000
sculpt_deactivate 2B9S

save $XXX-$chain-$num.pdb, all
" (out into) mutate.pml
pymol -qc mutate.pml 1 (out into) /dev/null

while [ ! -f $XXX-$chain-$num.pdb ] ; do
sleep 1
done

done
done