JonasR

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

Requires database set up with maintaindb.py.

JonasR

#!/usr/bin/env python

from __future__ import division
import pymongo as pym
import datetime as dt
import codecs
import re
import sys
import matplotlib.pyplot as plt
import numpy as np

JonasR

Processor Information:
    Vendor:  GenuineIntel
    Speed: 3499 Mhz
    8 logical processors
    4 physical processors
    HyperThreading:  Supported
    FCMOV:  Supported
    SSE2:  Supported
    SSE3:  Supported
    SSSE3:  Supported

JonasR

#!/bin/bash


for directory in `ls -d */`
do
	cd $directory
	for model in `ls | grep .eps`
	do
		MODELNAME=${model%.[^.]*}
		MODELNAME=${model}

JonasR

#!/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

#!/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

#!/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

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

##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