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At our university we are required to give a literature presentation. The presentation is 1 hour including time for questions. The goal of this exercise is to help students develop various skills that are valuable in a scientific career such as presenting, evaluating literature and answering questions. Good stuff.

I did my presentation and it really well except to one professor. According to my evaluation, I had confidently fabricated an answer and misled an entire audience. Fair enough, I make mistakes, but in this case I was right and had the literature to back it up. My scores were fine despite this one professor, but I wanted to discuss the issue. I was curious if the book and papers that supported my view were wrong. I wanted to learn.

I went to the head of session and asked who gave this evaluation. I was then told that the feedback was anonymous and they were not allowed to tell me. I then asked if he could ask the professor to contact me so that I could visit their office and discuss the evaluation. The head of session said that would be fine and sent out an email, but the professor never got in touch.

From this experience, I have also decided to no longer give anonymous feedback. I don’t want to hide. If the person who is getting my feedback disagrees, wants clarification, suggestions then great, let’s talk.

Scientific dialogue is invaluable and is reflected in our numerous publications and conferences.

I asked a faculty member of nearly 30 years why the policy existed and was told ‘this is the way we have always done it.’

Does your department give anonymous feedback? Do you find it helpful? Do you know why they keep that policy?

1) Open the desired coordinate files in Coot (click here if you need some help)
(You know you have been looking at structures too long when they start to look like faces.)

2) Under Calculate you have two methods of superimposing:
SSM Superpose (we will go with this option in this example: Calculate -> SSM Superpose…) or LSQ Superpose
Note: SSM Superpose stands for secondary-structure matching and if you need to do it outside of Coot there is a server.

3) Select which PDB you would like to move and apply:

The structures should now be superimposed:

CNS (Crystallography and NMR systems) is able to perform simulated annealing as well as generate a composite omit map, which is nice compliment to the CCP4 suite of programs (Phenix has similar features). In getting started, one must first create a generate file which is what the post will be covering via their website.

1) In your terminal type: cns_web (note: admin may have set up this command different)
Web browser should launch and select input files at middle left

2) Scroll down to generate.inp and click edit

A new window will open
3) Change ‘convert chainid to segid if chainid is left blank’ to True

Scroll down a ways to ‘general parameters’
4) Change: set bfactor flag to True AND set occupancy flag to True

Save and Exit

In your terminal
type: cns < generate.inp > generate.out &
Note: if you renamed your generate files then use them as your .inp
The ‘&’ symbol allows your cursor to be free

type: tail -f generate.out
This will allow to see the progress of the processing in your terminal
Doing this has allowed me to quickly see if my inputs have generate an error

Note: Depending on your needs using generate_easy.inp may be sufficient
Additional information can be found in the tutorial section of the CNS website.

When giving presentations, scientists typically don’t have trouble making their complicated work seem…well, complicated. The challenge is in making your message clear and audience appropriate.

Example:
How does life expectancy at birth and the number of children a woman has change by country over a period of one hundred years?

I felt a table with 8 point font coming on, but instead was amazed by this.
Hint: Hit play

Would making a graph like this be helpful in crystallography? Perhaps showing PDB entries by country over the last 60 years? I realize this tool may not be the most useful to our community, but it’s helpful in the sense that it inspires creativity. I now find myself contemplating how I can present research in a way that is clear, concise and creative. How can I help my data tell a story?

Tableau allows for the searching of protein folding patterns of substructures in the PDB structural database. This type of searching can be helpful in understanding protein structure, function and evolution.

The server searches using secondary structure elements and is capable of finding either an entire structure or a substructure of a larger structure (ref).

Tableau has a number of simple inputs (title, email, desired structure, output), however, you want to read the suggested tips. You can submit structures that contain multiple chains or domains, but it is not recommended. I submitted a number of structures and had a response time of about 3 minutes.

The server is also handy for tracking down fake structures.

The 2010 American Crystallographic Association (ACA) meeting in Chicago has been able to bring together the co-recipients of the 2009 Nobel Prize in Chemistry namely Venkatraman Ramakrishnan, Thomas Steitz and Ada Yonath.

The ACA reports that Venkatraman Ramakrishnan will be giving a plenary lecture on Saturday (7/24/2010) and Thomas Steitz will be giving a plenary lecture on Wednesday (7/28/2010). Ada Yonath will be speaking Wednesday morning on Macromolecules, Complexes & Assemblies.

Early registration ends May 31st.

If you are a US citizen attending graduate school then you may find this advice helpful.
Disclaimer: I am not a lawyer and/or CPA therefore they should be contacted before following any of this advice.

At the beginning of each year you have the ability to fill out a FAFSA, which essentially allows the government to determine whether you are eligible to receive financial aid. If you are eligible then you can receive a loan up to $8500 that can be subsidized. Subsidized meaning the loan does not accrue interest until 6 months after you graduate. My guess is that most graduate students are at least partially eligible who are not supported by their parents.

The numbers will vary depending by school, but let’s say a graduate student is making $25,000 a year. If it takes 5 years to complete your degree then you would be eligible to take out $42,500 (minus universities fees of ~1.5 percent on the loan).

A couple of years ago, savings accounts were paying about 5 percent interest, which on $42,500 is $2,125 (minus taxes) during your last year. If you are making ~$25 k a year then this is a significant amount of money. However, at the moment saving accounts and CDs are yielding about the same as the university fee so you could argue that it is not really worth the effort, fair enough.

The crowd that I think can really benefit are those that are planning on taking out loans (or currently have a loan). I have a number of colleagues that have taken out relatively high interest rate loans on vehicles or to attend medical school. The interest rates on these loans can be more than 12 percent. Currently, subsidized loans after the grace period are at 5.6 percent (ref).

Don’t forget this is a loan and must be paid back. You have to decide for yourself whether taking the additional risk is worth it.

The inability of a protein to be crystallized may be due to disorder regions. A work around to this problem is to truncate the protein. The question then becomes where should these truncations be made? A number of prediction servers have been created to address this problem (Nir put together a nice list here).

The metaPrDOS (meta Protein DisOrder prediction System) is convenient in that it predicts natively disordered regions of a protein chain from its amino acid sequence by seven utilizing
independent predictors (PrDOS, DISOPRED2, DisEMBL, DISPROT (VSL2P), DISpro, IUpred and POODLE-S) (pdf: ref).

The ability of this system led to a win at CASP7. (Does anyone ever lose at CASP?)

The inputs are straight forward:

A sample output can be found here (scroll down a little). I have been waiting almost 5 hours for an output, but still no luck.

Have you used any of these prediction servers? Did you like the results? What else are you using to decide where to truncate a protein?

We were able to put together a compilation of 36 resources that publish articles related to macromolecular crystallography. The result is a RSS feed that contains about 1500 articles and is constantly being updated. (what is a rss feed?) If the average article is 10 pages then this feed is currently at 15,000 pages — that’s a lot to sift through!

Fortunately, yahoo pipes allows a RSS to be filtered and only send you those that contain information of interest. In an effort to save you time, I am going to set up a customized feed for you. Consider it my way of saying ‘thanks for reading’.

What do you need to do?
Simply leave a comment with the keyword(s) that must be included within the journal article.

For example:
Sean
Keyword(s): hiv protease, crystallography, crystallization

How does this work?
I will then create a customized pipe from the 26 resources to your keywords and then reduce the number of entries to the 10 most recent articles. I will reply to your comment with a link that will generate your RSS feed. You can then copy/paste that link into your RSS feeder.

I am going to offer this help for the next 48 hours and then close the comment section.

I may have been putting off this post perhaps because it is not as fun reporting as good news.

I went to APS a couple of months ago to collect data on the miracle crystals (see link above). Cory from Emerald Biosystems was able to swing by (at nearly midnight!) and mount then plunge the crystals. Despite the channels being narrow, the mounting process is easy and by adding the appropriate buffer after opening the card there is no need to rush. I then transfered and screened the crystals. The result…

Salt crystals…

The crystals had a number of different morphologies, but unfortunately they were all salt crystals.

Although I have seen many others have the fun of collecting on salt crystals this was my first time. If you haven’t had the experience it is like watching a unicorn die.