] Tips and Tricks - for the wet and dry labs

Curry Lab

Biophysics Section
Division of Cell and Molecular Biology
Department of Life Sciences
Faculty of Natural Sciences

Tips and Tricks

This page is as a repostitory for a variety of topics related to the business of doing science in the wet and dry labs (with a bias towards methods related to structural and molecular biology). There is a mix of generic and particular skills or techniques. I will endeavour to keep it up-to-date!

Please feel free to email me if you have comments or questions.

Crystallography Blog - P212121

P212121 (named for the most common space-group that occurs in protein crystals) is a great repository of tips and tools for macromolecular crystallography. I highly recommend subscribing to the rss feed.

How to write

The value of developing writing skills cannot be over-emphasised! Well-written papers are more likely to be accepted, well-written grants funded (no guarantees, alas). Despite this, writing skills still do not receive enough attention during UG and PG scientific training. Ultimately there is no substitute for practice, followed by... more practice!

For some very valuable guidance on how to approach writing scientific papers try this article in J. Cell. Biol. or this one in EMBO Reports (subscriptions may be required).

Another useful article appeared in J. Clin. Invest.; this one is written from the editor's point of view and gives some good advice on the process of submission and reponding to referees' comments.

How to give a presentation

Among other things, effective communication requires (i) a good understanding of and respect for the needs of the audience and (ii) an appreciation of the power and limitations of the presentation software that is most widely used, i.e. Microsoft's Powerpoint (though, personally, I prefer Apple's Keynote). A good performance will usually require plenty of rehearsal (or lots of previous experience!). It can seem a daunting challenge for novices but many of the worries can be neutralised by effective preparation.

If you click on the image to the right, you can find a short presentation (pdf format - 2.4 MB) that I prepared when teaching students and postdocs at Imperial about how to give a good talk. It's not comprehensive but should help you to avoid some of the more common pitfalls.

See also this web-site at PLoS Computational Biology which gives 10 valuable rules to follow - many of which overlap with the points made in my slideshow!

Alternatively, head over to the Life of a Lab Rat blog for an excellent discussion of the finer points of presentation.

Powerpoint Tips

Powerpoint is a sophisticated program that is relatively easy to use, especially for simple presentations.

If you want to learn a bit more about how to put together a stylish presentation and to make efficient use of some of the powerful drawing tools within the program, click on the image on the right to download a Powerpoint presentation (0.5 MB). You may also want to consult the section on "How to give a presentation" above for general information on how to get your message across.

How to use PyMOL

PyMOL is a fantastic program written by Warren Delano for looking at macromolecular structures (proteins, RNA, DNA) and making beautiful figures for publication and presentation.

The program is best used once you have at least a rudimentary understanding of the pdb files that contain the molecular co-ordinates). To help you get going, you can click on the image on the right to download a presentation (4.7 MB pdf) that I put together to give a 40-50 minute introduction to the program (now slightly updated - Mar 2009).

It covers opening a pdb file and displaying a molecule, with a brief description of some of the major menu items. The presentation also gives some explanation of how to make publication-quality figures with the program. Though I gave the presentation alongside "live" demonstrations of the use of the program to show how features worked, I think that it can also be useful as a stand-alone experience. Good luck! Please feel free to ask for clarification or to suggest improvements.

If you would like to have copies of the files used in this tutorial, get them from here as a zipped file. Please let me know if you have any problems with the file.

Making Movies with PyMOL

With a bit of care, it is possible to make very useful movies or animations of protein structures using PyMOL. Although the program has in-built tools for creating movies, I prefer to use the movie.py script from the rTools package, since I think this provides a more intuitive way to work.

You should only attempt this once you have some familiarity with the general loading and drawing commands within PyMOL (see entry above to get started). On the right you can click on the image on download a presentation (2.4 MB pdf) that I used to give a 45 minute introduction to movie-making with the program. You can also download a Quicktime movie (large and small filesizes available) of the presentation which incorporates the animations that were demonstrated and explained. (Note: Once you have opened the Quicktime movie, just click repeatedly to step through the slide-show. Please be aware also that these movies don't play the animations quite as smoothly as they work in real time.)

The presentation gives some initial guidance on 'best practice', shows how to obtain and install the movie.py script and then works through a couple of example scripts for generating a series of images that will be turned into a movie. Thereafter I deal with assembling the images into a movie (on Mac and PC) and show how they can be incorporated into PowerPoint.

 

PyMOL_movies.12fps.mov (5.3 MB)

PyMOL_movies.24fps.mov (13.4 MB)

Papers - organise your pdfs

Mac only I'm afraid, but Papers is a brilliant piece of software for organising pdfs of scientific papers.

Written by Alexander Griekspoor and Tom Groothuis (aka Mekentosj), the program works a bit like iTunes. It's very user friendly and very powerful. You can import papers from your hard-drive or directly from online libraries such as Pubmed. Though I still prefer to read from a piece of paper than from the screen, the program has a good "full-screen" mode. If I want to work on a manuscript of my own at home, it's very convenient to be able to take my collection of papers with me on my laptop.

Update: There is now even a version of Papers for the iPhone and iPad, so you really can take your library of pdfs anywhere. The iPhone screen is admittedly a bit small for prolonged use but it's a useful application for quickly checking things when you don't have your laptop with you.

Keep track of the scientific literature using RSS feeds

We all struggle to keep abreast of new publications, but if you're a regular user of Pubmed, you can use RSS feeds so that your Web-browser notifies you as soon as new papers in your chosen research area appear.

Here are the instructions:

  • Use a browser that supports RSS (most modern ones do)
  • Do a search within Pubmed
  • When the results appear, use the "Send to:" drop-down menu and choose RSS feed
  • Click on Create feed
  • Click on the orange XML icon
  • Bookmark the resulting URL (should start with feed://...)
  • Ideally add this bookmark to the browser toolbar - so the alerts are always visible

Webcutter - primer design for faster mutagenesis

Webcutter 2.0 is a great online source for DNA primer design, especially when you need primers for site-directed mutagenesis, e.g. using Strategene's Quikchange.

The program helps you to incorporate into your primer, along with your desired mutation, translationally silent restriction sites that will allow you to quickly test if your mutagenesis reaction has worked.

Nov 2010
http://www.bio.ph.ic.ac.uk/~scurry/