MOE 2019.01 now available

New capabilities include ensemble protein property calculations, MOEsaic session sharing, determination of conformer populations using NOE Data and AMBER thermodynamic integration. See and

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CSD System 2019 Release

Test blog entry here

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Blogs server upgrade

We’re finishing off migrating the vast majority of our infrastructure servers from Debian to Ubuntu, and the blogs server is one of the many things that has had to be replaced. This post is to test the new blogs virtual machine.
The upside of doing this migration is Ubuntu Long Term Support releases have a longer lifetime than Debian releases, so in theory we’ll only have to upgrade servers once every five years in future rather than every two.

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When is nothing something?

We use devmon to automatically monitor a variety of things on our network, including our uninterruptible power supplies (UPSs) that ensure our core infrastructure is able to withstand short power outages.
Our UPSs should perform a self-test routine every two weeks, and thus I wanted to have our automated monitoring report on whether or not a self-test had been performed sufficiently recently. The UPSs report the date they were last tested in the format MM/DD/YYYY (i.e. today, the 8th of June 2017, is 06/08/2017), and so I needed to parse dates of that format so I could calculate the number of days since the last self-test.
Ordinarily the advice on performing any sort of date calculation when programming is “use a date library”: date calculations are notoriously difficult to get totally right, and you’re normally better off using a library that someone has written and which has already been thoroughly tested. But that’s not an option inside devmon: one can perform basic mathematical and string manipulation operations, but little else.
I wrote the monitoring report about a week ago, and it had been working fine – but I noticed that it had stopped reporting today. The first step in parsing the date is to take a string like 06/08/2017 and extract characters 1 and 2, then 4 and 5, then 7 to 10 and store them as the month, day and year respectively.
An oft-used convention in programming languages is that numbers that start with a leading zero should be interpreted as octal (base 8) numbers. Thus, in octal, the decimal numbers 1 to 10 are 01, 02, 03, 04, 05, 06, 07, 010, 011, 012.
You might now see the problem: 08 is not a valid octal number, so the underlying code stopped working today! Running devmon in debug mode quickly let me find the reason for the problem:
Illegal octal digit ‘8’ at (eval 13) line 1, at end of line
and so the fix was simply to remove any leading zeroes from the month and day.

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Network cable installation

We’re in the midst of refurbishing one of our server rooms, and as part of this we’re installing many network cables. If you didn’t know, network cables have eight wires inside them, and these are twisted into four pairs. So in order to connect the wires on to the panel you have to untwist an awful lot of wires. If you’ve ever suffered from carpal tunnel syndrome, you’ll know that one needs to be very careful when performing repetitive motions with one’s hands and wrists.
We wanted a tool that was small (because it has to be used in fairly close quarters), and which we could use to grip and untwist small wires (preferably not metal, because that could risk damaging the plastic insulation). After a little searching, we found the ideal tool to help with this task:
It’s too early for snow in Cambridge yet, but we were willing to overlook that given just how much easier the small snowman makes installing all of these network cables!

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Gaussian and Gaussview software

Gaussview 5 for Mac and Linux is now freely available to researchers in
Chemistry as the graduate education office and computer office have bought a site licence for these packages.
Gaussview can be used on its own, but is more useful when paired with Gaussian. We already have a site licence for Gaussian 03 and 09 for Linux which all chemists can use (in return for a small contribution to the licence costs in the case of 09 for Linux).
We now also have access to Gaussian 09 for Macs, as another department has purchased a site licence which covers the whole University and Chemistry has acquired a media set to go with that.
If you would like to use any of these packages then please go to the
appropriate web page for details on how to get them:

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Group computer reps meeting, August 17th 2016

On August 17th we held one of our semi-regular meetings with the Department’s group computer reps. The links presented are available on our website, which also includes links to the slides used in our past meetings.

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ZendTo – sending large files

ZendTo is a piece of software intended to let members of the Department send or receive files that are too large to attach to emails: it provides a website that lets people drop off files that can be collected by members of the Department, as well as allowing authenticated members of the Department to drop off files for collection to any email address. All drop-offs are automatically deleted after 14 days.
The service can be accessed at and some Department-specific documentation is at

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TeamViewer and remote access

Some of you may have read a recent story about possible security problems concerning TeamViewer, for example:
There are a number of supported remote access technologies in the Department, as described at
Our recommended method for remotely connecting to Windows computers is to use our VPN service and then use Remote Desktop. For remotely connecting to Linux computers, please see our documentation on using VNC.
The advantage of using the recommended Departmental services rather than 3rd-party services such as TeamViewer is that it ensures that all of your network traffic is transmitted only through trusted Departmental servers rather than through a potentially unknown 3rd party.

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Software updates for managed Windows computers

Windows computers in the Department have their installed software managed by WPKG. Software that has been recently added to the list of available packages includes:

  • WinDirStat – a free utility for producing a folder-by-folder report of disk usage
  • MarcEdit – a tool for editing MARC data files
  • ExamDiff – a tool for showing the differences between two files (will be familiar to anyone who has used the Linux diff command line tool)

The full list of software that is available for installation through WPKG is at

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