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Lab server setup - Ubuntu 12.4

With a recent change of machines in the lab, I thought that I should update the backup server according to reflect the new machines. However, upon inspection the backup server OS hard drive had died...

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Logarithmic backups on a linux server

This is the second part of the lab server setup guide. Mainly for my own memory purposes, but if you find it useful then so much the better. SynchronizationAs previously discussed all of the machines...

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Troubleshooting a non-connecting Bruker ELEXSYS spectrometer

Recently in the lab we've had some problems thanks to a helpful software update rendering it impossible to connect to a spectrometer. This troubleshooting provides a record of my steps to diagnosing...

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Xepr license work around

Disclaimer: the author does not condone piracy but this may be used as a temporary measure​As readers of my work-sided blog posts will be aware, I've had some recent problems with spectrometers and...

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HTC Desire headphone jack fix

This morning on the way to work I got down to the road, plugged in my earphones to my phone and hit play on Spotify. Only for some horrible, tinny, quiet music to come out. It seemed that the phone...

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PyMOL visualising MMM rotamers

 This morning whilst writing some reports I wanted to show some rotamer populations of my spin label attached to the protein. Whilst MMM provides visualisation, and having had discussions with Jeschke...

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e2af

E2AF or "EPR 2 ASCII folder" is a folder version of E2A, whereby a folder of Bruker EPR files are converted to ASCII data files (readable by any operating system), by default the conversion is to *.csv...

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Ghosts of Xmas past

 It has been some time since my last blog post, but this is more a reflection of my philosophies than inabilities. It has been a very many years since I started blogging and it has largely been my...

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EasyRefiner

Faced with fitting well over 30 experiments at room and low temperature at multiple frequencies, as all of my experiments are spin-labelled mutants of the same protein then surely their EPR properties...

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What I love about science...

...is the ability that every day provides the opportunity, and more often than not, allows you to realise what a colossal idiot you are.And not just about the simple stuff, the every day mundane things...

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addnoise

This script allows the user to add noise to a spectrum, in a manner almost exactly opposite to smoothing data. The script random adds noise to each data point of a spectrum within the range of +/- a...

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BrukerWrite - Write Bruker BES3T files

This script allows for the writing of cw-EPR Bruker BES3T files (.DTA/.DSC) files from MATLAB onto your computerThe script uses a graphical user interface to select file name and location, so minimal...

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Clone an (openSUSE) machine and make it functional

In the last week I've had some need to setup some new PCs to control some of our machines in the lab. The problem being that the control interface between machine and PC is quite complicated and uses...

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Getting an openSUSE machine online

This week I've been cloning machines, but each new machine has slightly different hardware, even if it's just a MAC address or serial number.So, a quick disclaimer I'm using openSUSE 11.3 and so things...

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Take back the ordinary

It was once said that the difference between the ordinary and the extraordinary is that little bit extra. A potent statement, and one full of wisdom, but one I find myself disagreeing with more and...

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pdbimport

 pdbimport loads a PDB file into MATLAB, something which is very difficult to do yourself if you dont have the very expensive Mathwork's Bioinformatics Toolbox. The difficulty largely arising due to...

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EPR Converter (e2a)

The Bruker spectrometers output data by default in the Bruker BES3T format, which whilst being perfectly usable is not recognisable by most operating as standard.This script was originally written for...

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pdbexport

Following on from pdbimport, pdbexport takes a PDB structure that has been loaded into MATLAB and exports it to the file structure as a .pdb fileFile naming and location is handled using a graphical...

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PyMOL with Ubuntu 11.10 rendering problems

Recently my (Ubuntu 11.10 64bit) machine stopped playing nice with PyMOL and whenever I tried to render or move an object I was facing a >40 second render time, while both of my CPU cores jumped to...

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PyMOL visualising binding interfaces

Today I've been trying to come up with a nice way of visualising the binding interface between protein-protein or protein-DNA complexes. What follows is a quick little walk-through mostly for my own...

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DEERextract - get data from DeerAnalysis

DeerAnalysis is a program from the team at ETH Zurich that allows for the easy conversion of DEER / PELDOR data into distance distributions. The program itself runs within MATLAB which is renowned for...

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Moving apps from the Android phone memory to SD card: HTC Desire

 So I've had my HTC Desire now for approxmately 2 years now and whilst it has served me well I've had a bug bear with it for a long time. Essentially the phone has only 148 MB of internal storage and...

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Reflection of a conference

The science world is an odd one. Almost all ideas are communicated through one of two means, tried and tested means that show no sign of changing any time soon. The first is that of academic papers or...

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Motivation and a mission

 The church would have you believe that Sunday is the God given day of rest, whilst the business world would tell you that it was rather the Bank Holidays that were sacrosanct. Well today I tell you...

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cwViewer

 cwViewer is a tool for the easy opening, analysis, manipulation and plotting of cw EPR data and superceeds the previous function cwPlotterWith an intuitive user interface, users can quickly create...

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Savitzky-Golay - sgol

The Savitzky-Golay smoothing function essentially applies a local polynominal fitting routine to a series of data points to then find the smoothed data points. This has the benefit that for sharp...

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Red car...

Today I had to take the car to a tyre garage type place having picked up a puncture in the shape of a massive thorn over the weekend. Now I've never been a great advocate of the intelligence required...

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(Anti-) Social Media

Today it is much more difficult to get up than it was 10 years ago, and that's not just because we're all getting older. 10 years ago chances are that every morning started with the same thing; hitting...

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Frozen in space and time

  Now don't get me wrong, I love my job, I really do. I don't think there are many other opportunities in this world where I could get to be a biochemist, chemist, physicist, engineer and software...

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Annoying the French

Sometimes you get to the end of a conversation and you realise just how weird it got for a moment somewhere in the middle. And really by the end of it, you're so far from whence you started that the...

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