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JonasR

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@JonasR
JonasR / gist:5970916
Created July 10, 2013 22:52
Complete system report for Dota 2 Issue #37
View gist:5970916
Processor Information:
Vendor: GenuineIntel
Speed: 3499 Mhz
8 logical processors
4 physical processors
HyperThreading: Supported
FCMOV: Supported
SSE2: Supported
SSE3: Supported
SSSE3: Supported
View UP000005640_9606_sing.fasta00002.snap2
A1R => 48 51 | 60 39 | 30 69 | 68 31 | 34 65 | 44 55 | 64 35 | 55 44 | 52 47 | 62 37 | sum = -4
A1R Neutral 0 53%
A1N => 65 34 | 73 26 | 53 46 | 85 14 | 55 44 | 61 38 | 78 21 | 75 24 | 68 31 | 77 22 | sum = -39
A1N Neutral 3 66%
A1D => 43 56 | 53 46 | 29 70 | 62 37 | 31 68 | 42 57 | 61 38 | 54 45 | 43 56 | 60 39 | sum = 4
A1D Neutral 0 53%
A1C => 84 15 | 82 17 | 71 28 | 94 5 | 75 24 | 77 22 | 86 13 | 89 10 | 82 17 | 88 11 | sum = -66
A1C Neutral 6 82%
A1Q => 63 36 | 70 29 | 47 52 | 83 16 | 51 48 | 58 41 | 76 23 | 74 25 | 64 35 | 75 24 | sum = -33
A1Q Neutral 3 66%
@JonasR
JonasR / gist:3557814
Created August 31, 2012 19:24
create trajectory animations
View gist:3557814
#!/bin/bash
pymol -c createTrajectories.pml
rm mov0001.png
convert -delay 25 -dispose Background -loop 0 *.png TSD_178H_traj.gif
@JonasR
JonasR / gist:3557912
Created August 31, 2012 19:31
create plots, comparing b factor on all atoms and on c alpha only
View gist:3557912
load ../../referenz_close_lessshallow.pse, ref
load ../../Output/WT/out/WT.ca.bFactor.pdb , bfca
align bfca, REFERENZchaina
delete REFERENZchaina
load ../../Output/WT/out/WT.prot.bFactor.pdb , bfprot
align bfprot, bfca
zoom bfca, buffer=-6
@JonasR
JonasR / gist:3557972
Created August 31, 2012 19:36
Create all the base data for the MD runs
View gist:3557972
#!/usr/bin/perl
use strict;
my $file=shift;
my $refFile;
my $outName=shift;
my $fileName=$file . "_md";
$refFile= $file . "_solv.pdb";
$file= $file . "_md.xtc";
@JonasR
JonasR / gist:3557978
Created August 31, 2012 19:37
Call script for creating base data
View gist:3557978
#!/bin/bash
perl /media/share/mapra/mapra/MD_perl/perly.pl /media/share/mapra/mapra/178H/mdrun_2gjx178H/2gjx178H /media/share/mapra/mapra/Output/178H/out/
@JonasR
JonasR / gist:3557985
Created August 31, 2012 19:38
create plots
View gist:3557985
#!/bin/bash
for directory in `ls -d */`
do
cd $directory
echo now $directory
echo "First part"
for model in `ls | grep .xvg | grep -v -P "\.eps$" | grep -v rama|grep -v pressure|grep -v temperature | grep -v potential|grep -v totalEnergy`
do
@JonasR
JonasR / gist:3557996
Created August 31, 2012 19:38
Convert plots to png
View gist:3557996
#!/bin/bash
for directory in `ls -d */`
do
cd $directory
for model in `ls | grep .eps`
do
MODELNAME=${model%.[^.]*}
MODELNAME=${model}
@JonasR
JonasR / gist:3557863
Created August 31, 2012 19:27
create trajectory pngs
View gist:3557863
##Thanks to Hemochromatosis journal for help
load ../../referenz_close_lessshallow.pse, ref
load ../../Output/178H/out/178H.pdb, traj
align traj, REFERENZchaina
zoom traj, buffer=-6
delete REFERENZchaina
#Representations and colouring
hide everything, all
View plotRMS.R
d <- read.table("1207270221251193.7.rmsmod_onlyca")
x1 <- seq(from=1,to=131)
x2 <- seq(from=132, to=492)
y1 <- d$V1[1:131]
y2 <- d$V1[132:492]
col1 <- rep("red", 131)
col2 <- rep("blue",361)