JonasR

#!/bim/bash

echo "This even allows versioning and forking!"

JonasR

P06865 1 M V
P06865 39 L R
P06865 58 C Y
P06865 127 L R
P06865 170 R W
P06865 178 R H
P06865 210 S F 
P06865 258 D H
P06865 451 L V
P06865 482 E K

JonasR

>P06865
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY
LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK
EVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEF
MSTFFLEVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLL
DIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPW
YLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAV
AERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT

JonasR

M1V
L39R
C58Y
L127R
R170W
R178H
S210F
D258H
L451V
E482K

JonasR

###Create base file
fetch 2gjx
select chainA, chain A
select rest, not chainA
remove rest

select firstDomain, resi 1-166
select secondDomain, not firstDomain
remove firstDomain
zoom secondDomain

JonasR

#!/bin/bash

for i in R178H R178C P183L D207E S293I F434L L451V E482K L484Q E506D; do
        perl prepForSQRWL2.pl -i 2gjxA_sequence -mut $i > SCWRL_$i.sequence
done

for i in R178H R178C P183L D207E S293I F434L L451V E482K L484Q E506D; do
        /opt/SS12-Practical/scwrl4/Scwrl4 -s SCWRL_$i.sequence -i ../2gjxA_secondD.pdb -o SCWRL_$i.pdb &>> SCWRL.log
done

JonasR

#!/usr/bin/perl


use Getopt::Long;
our $opt_f = ();

sub usage {
        printf "Usage: $0 [flags] file...\n";
        printf "flags:\n";

JonasR

<TITLE>FOLDX_runscript;
<JOBSTART>#;
<PDBS>#;
<BATCH>list.txt;
<COMMANDS>FOLDX_commandfile;
<BuildModel>#,individual_list.txt;
<END>#;
<OPTIONS>FOLDX_optionfile;
<Temperature>298;
<R>#;

JonasR

#!/bin/bash

ln -sf /opt/SS12-Practical/foldx/rotabase.txt
/opt/SS12-Practical/scripts/repairPDB ../preparation/2gjxA_secondD.pdb > 2gjxA_secondD_repaired.pdb
/opt/SS12-Practical/foldx/FoldX.linux64 -runfile run.txt

JonasR

RA178H;
RA178C;
PA182L;
DA207E;
SA293I;
FA434L;
LA451V;
EA482K;
LA484Q;
EA506D;