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Processor Information: | |
Vendor: GenuineIntel | |
Speed: 3499 Mhz | |
8 logical processors | |
4 physical processors | |
HyperThreading: Supported | |
FCMOV: Supported | |
SSE2: Supported | |
SSE3: Supported | |
SSSE3: Supported |
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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% |
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#!/bin/bash | |
pymol -c createTrajectories.pml | |
rm mov0001.png | |
convert -delay 25 -dispose Background -loop 0 *.png TSD_178H_traj.gif |
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#!/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 |
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#!/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/ |
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#!/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"; |
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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 |
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#!/bin/bash | |
for directory in `ls -d */` | |
do | |
cd $directory | |
for model in `ls | grep .eps` | |
do | |
MODELNAME=${model%.[^.]*} | |
MODELNAME=${model} |
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##Thanks to Hemochromatosis journal for help | |
load ../../referenz_close_lessshallow.pse, ref | |
load ../../Output/178H/out/178H.pdb, traj | |
align traj, REFERENZchaina | |
zoom traj, buffer=-6 | |
delete REFERENZchaina | |
#Representations and colouring | |
hide everything, all |
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d <- read.table("1207270221251193.7.rmsmod_onlyca") | |
x1 <- seq(from=1,to=131) | |
x2 <- seq(from=132, to=492) | |
y1 <- d$V1[1:131] | |
y2 <- d$V1[132:492] | |
col1 <- rep("red", 131) | |
col2 <- rep("blue",361) |
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