JonasR

#!/bin/bash
pymol -c  createTrajectories.pml
rm mov0001.png
convert -delay 25 -dispose Background -loop 0 *.png TSD_178H_traj.gif

JonasR

d <- read.table("1207270221251193.7.rmsmod_onlyca")


x1 <- seq(from=1,to=131)
x2 <- seq(from=132, to=492)
y1 <- d$V1[1:131]
y2 <- d$V1[132:492]
col1 <- rep("red", 131)
col2 <- rep("blue",361)

JonasR

#!/bin/bash

for dir in 7 8 9 10 11
do
    echo "Currently doing $dir"
    cd $dir
    grep -P --only-matching "CA\s+0\.\d+" 1207270221251193.$dir.rmsmod | grep -P --only-matching "0\.\d+" > 1207270221251193.$dir.rmsmod_onlyca
    R CMD BATCH plotRMS.R
    convert plot.eps plot.png
    cd ../

JonasR

#!/bin/bash

for dir in 7 8 9 10 11
do
    echo "Currently doing $dir"
    cd $dir
    pymol -c  createPNGs.pml
    rm mov0001.png
    convert -delay 10 -dispose Background -resize 50% -loop 0 *.png animation.gif
    cd ../

JonasR

##Thanks to Hemochromatosis journal for help
load ../../../2GK1A_NGTdeleted_referenceorientation.pse, reference
load ./1207270221251193.7.pdb, modes
align modes, 2GK1A_NGTdeleted
zoom 2GK1A_NGTdeleted, buffer=-8.5
delete 2GK1A_NGTdeleted

#Create secondary structure annotation for elnemo output
dss modes

JonasR

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fod/mapra/agrosRuns/WT/FINAL/WT.out
#SBATCH -D /home/hpc/pr58ni/di34fod/mapra/agrosRuns/WT/FINAL/
#SBATCH -J 2gjxWT_MD_FIN
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=reeb@in.tum.de
#SBATCH --export=NONE

JonasR

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fod/mapra/agrosRuns/P182L/P182L.out
#SBATCH -D /home/hpc/pr58ni/di34fod/mapra/agrosRuns/P182L/
#SBATCH -J 2gjxP182L_MD
#SBATCH --partition=mpp1_inter
#SBATCH --get-user-env
#SBATCH --ntasks=16
#SBATCH --mail-type=end
#SBATCH --mail-user=reeb@in.tum.de
#SBATCH --export=NONE

JonasR

#!/bin/bash 

scp reeb@i12k-biolab05.informatik.tu-muenchen.de:/mnt/home/student/reeb/git/masterprak/Tasks/7_StructBasedMutAna/SCWRL/SCWRL_R178H.pdb ./R178H/2gjx178H.pdb
scp reeb@i12k-biolab05.informatik.tu-muenchen.de:/mnt/home/student/reeb/git/masterprak/Tasks/7_StructBasedMutAna/SCWRL/SCWRL_P182L.pdb ./P182L/2gjx182L.pdb
scp reeb@i12k-biolab05.informatik.tu-muenchen.de:/mnt/home/student/reeb/git/masterprak/Tasks/7_StructBasedMutAna/preparation/2gjxA_secondD.pdb ./WT/2gjxWT.pdb

JonasR

#!/bin/bash
function iterate()
{
        BASEI=$1
        /opt/SS12-Practical/minimise/minimise $BASEI.pdb ${BASEI}_it1.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it1.pdb ${BASEI}_it2.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it2.pdb ${BASEI}_it3.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it3.pdb ${BASEI}_it4.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it4.pdb ${BASEI}_it5.pdb &>> ${BASEI}_it.log
}

JonasR

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