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JonasR

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  • AbbVie
  • Germany, Remote
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@JonasR
JonasR / gist:2919934
Created June 12, 2012 20:29
helloworld
View gist:2919934
#!/bim/bash
echo "This even allows versioning and forking!"
@JonasR
JonasR / gist:2944224
Created June 17, 2012 11:15
PolyPhen 2 Batch file
View gist:2944224
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
JonasR / gist:2944226
Created June 17, 2012 11:16
P06865 sequence
View gist:2944226
>P06865
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY
LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK
EVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEF
MSTFFLEVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLL
DIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPW
YLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAV
AERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT
@JonasR
JonasR / gist:2944236
Created June 17, 2012 11:20
SIFT mutation input file
View gist:2944236
M1V
L39R
C58Y
L127R
R170W
R178H
S210F
D258H
L451V
E482K
@JonasR
JonasR / prepareFiles.pml
Created June 21, 2012 16:02
Prepare 2gjx to be used in structure based mutation analysis
View prepareFiles.pml
###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
JonasR / allmuts_*.sh
Created June 21, 2012 16:18
Preparing sequences for SCWRL and then calling SCWRL on them
View allmuts_*.sh
#!/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
JonasR / prepForSQRWL2.pl
Created June 21, 2012 16:19
Lowercase sequence and create one sequence per mutation
View prepForSQRWL2.pl
#!/usr/bin/perl
use Getopt::Long;
our $opt_f = ();
sub usage {
printf "Usage: $0 [flags] file...\n";
printf "flags:\n";
@JonasR
JonasR / run.txt
Created June 22, 2012 00:55
FoldX runfile
View run.txt
<TITLE>FOLDX_runscript;
<JOBSTART>#;
<PDBS>#;
<BATCH>list.txt;
<COMMANDS>FOLDX_commandfile;
<BuildModel>#,individual_list.txt;
<END>#;
<OPTIONS>FOLDX_optionfile;
<Temperature>298;
<R>#;
@JonasR
JonasR / callFoldx.sh
Created June 22, 2012 00:55
Call Foldx
View callFoldx.sh
#!/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
JonasR / individual_list.txt
Created June 22, 2012 00:57
FoldX Mutation file
View individual_list.txt
RA178H;
RA178C;
PA182L;
DA207E;
SA293I;
FA434L;
LA451V;
EA482K;
LA484Q;
EA506D;