The focus of this site is largely on macromolecular crystallography, but for our friends with mirror planes this may of interest (feel free to pass this on). Bruker is loaning out a SMART X2S for six months that includes delivery and installation. The SMART X2S is a highly automated crystal-to-structure small molecule X-ray system.
To enter, write a 1-3 paragraph summary of why you think the SMART X2S is the ideal tool for your research and/or teaching. The contest ends at the end of the year. The official rules are listed at Bruker.
It is the beginning of fall semester and the air is full of first year graduate students talking about how they are going to finish their PhDs early.
Being new to the field, my guess is they are unaware of the existence of arbitrary rules. These rules have developed over time, being passed down from one graduate student to another as a sort of unwritten code.
(are you enjoying reading the unwritten?)
Interaction with Fellow Students:
Arbitrary rules exist to teach first year students to respect authority. They are not written down or verbalized, however you will be scolded for not knowing them.
Example:
“Where is the HEPES buffer?” “It should be in the bottom of the fridge.”
“Yeah, checked there…” 1st Yr: Oh, I put it on the top shelf
“What! You’re only supposed to put salts on the top shelf. All Good buffers are supposed to be kept on the bottom shelf.”
(Thanks a lot 1st year for turning my day into a living hell)
In addition, arbitrary rules teach 1st year students to respect their elder students.
Example:
“Where is the TEV protease?”
(The answer will depend on the seniority of the person asking):
1st year: “In the -80.”
2nd year: “2nd shelf in the -80″
3rd year: “2nd shelf from the top in the -80″
4th year: “2nd shelf from the top, behind Jill’s box in the -80″
5th year: “Let me show you”
The first year gets the pleasure of digging through the entire -80, while the 5th year is shown where the TEV protease is located.
Interaction with Your Lab:
The first couple of weeks in the lab are going to be like a depressing Easter egg hunt.
To give you a false sense of security, we have labeled most of the drawers and cabinets. However, you will soon realize that the cabinets that hold what you are looking for, do not have a label.
The way you learn this lesson is by looking through every cabinet and drawer, again and again. For your personal enjoyment, we have also placed deceiving labels on some cabinets, like ‘Glassware’, which will (obviously) contain plastic funnels.
Interaction with Your Boss:
Arbitrary rules are complex enough that your boss will never figure them out.
I find it funny when 1st year students think they can get around the arbituary rules. They will ask your boss where an item is located and after 5 minutes of failing to find anything what they are looking for, they will ask one of the more senior students.
This makes the 1st year feel a little off because they’ve seemingly wasted the boss’s time when they could have just asked a senior student.
The cryoprotectant database for protein crystals is a great resource. The database is coming up on 2000 entries and has a number of search functions:
Click on the ‘ex.‘ button to display the search terms Note: To save time, I copy paste the keywords directly from the menu that appears
The reason that this resource is so delightful is that it searches out, not only the cryprotection method, but the freezing method used from literature.
How can this database help you?
A good way to use the database, is if you have a crystallization condition and want an idea of what has been used as a cryoprotectant with that condition. In some cases, you need to click on the protein name to see the cryoprotectant used, if it is not mentioned in the freezing method.
Suggestion Box: I wish the freezing method adjusted to fit my monitor to eliminate the need to scroll from side to side. I would also like to have a simple toggle for the ‘Crystallization Method’ section. A toggle would save time by reducing the need to type and the time needed to figure out what to input.
I was having a good conversation at the ACA this year with a couple of friends when a person I had never met walked up. I introduced myself, offered the customary handshake and, yet, got the following response: “Why should I care?”
Ah, nothing like sticking your neck out there only to find you’ve come across someone who is completely inconsiderate. So to answer your question:
1) “Do unto others as you would have others do unto you.”
You should treat others with respect, regardless of whether or not you know them. I am sure you have heard this phrase before, but unfortunately not everyone seems to get it – so let me break it down:
a) You should suck up because this new acquaintance will…
write your recommendation letter
set up a collaboration
review your grant.
be interviewing you for your next job, according to Murphy’s law
guess who is going to save the day when you have problems collecting data on the weekend, probably a post doc.
administrators can make your life wonderful or hell. Yelling at the person who determines this is stupid
if you need a gram of pure protein, you are going to want productive happy technicians and graduate students
if you want the best people to work for you then you need to create the best working environment
you never know who is going to be successful and play a role in determining your future
make friends on your way up because you will need them on the way down
2) It doesn’t really matter what you say about yourself, it matters what people say about you. This is the reason why many jobs require a letter of recommendation. Of course, you can’t control what others say (unless you are into waterboarding) so make sure they only have good things to say about you.
3) You’re not only representing yourself, but also your university or company.
4) For those that don’t care may your burned bridges light the way to your future.
Can your research benefit from creating an online community? Since the focus of this session is education, lets think about how we could improve, and possibly change, the classroom learning environment. Here’s one for professors: Twitter.
If you’re not familiar with Twitter, it is a public real time instant messaging service. Why not use Twitter in the classroom? Some classes have, literally, hundreds of students, many of which don’t ask questions. They’re intimidated by the size of the class and are worried that they’ll sound stupid. So, they don’t ask questions. Twitter could solve this problem by giving these “shy” students the ability to ask questions by using their laptops or cell phones. They simply instant message their questions to the professor, the professor can review the questions and address them at the start of the next lecture or possibly improve the lecture for next year (or answer them in real time if he or she is feeling ambitious).
What Twitter creates is a 2-way street. By embracing this idea of equal communication, students can get the most out of their lectures. Twitter makes the professor more Accessible to the students. It would be an exciting Change and, ideally, improve Education by giving the professor another way to Serve the students.
Note: After giving this presentation, I was approached by a University of Toledo professor who shared that he is going to implement this idea in his classroom. Cool!
The people becoming involved in crystallography are coming from a more mixed background. I can safely say there are going to be more biochemists, biophysicists and biologists using crystallography in the future. As such, we need to develop a better, more user-friendly system so those who are less familiar with crystallography don’t slip up.
Note: In an effort to create an online community for young scientists to communicate, a Facebook group was created: ACA Young Scientist SIG— a result of a great discussion at this year’s ACA.
The unfortunate example would be the Science papers that were retracted a few years back. That was an embarrassment to the entire structural community. It made us look sloppy. There’s no reason for that to happen, especially with the availability of the internet. We have the unique opportunity to build a stronger, more efficient and more resourceful community online. Bringing about this kind of change is going to require some innovative ideas and dedicated people. Thank you for your time.
You have told them or heard them, but either way it is good to know what everyone is talking about. Ok, so these are not all lies, but hopefully you get the idea…
1) “It shouldn’t be that hard.”
Really means, “I am pretty sure that it is not impossible.”
2) “It won’t take that long.”
Whatever magical timeline has been presented, just triple it.
3) “Could you ______”
Science is passive agressive this means ‘do it or else.’
4) “I would love to see _____ in your dissertation”
This request will never stop and will be replaced by ‘paper’ soon after graduating
5) “What I would like us to work on…”
It is going to be you, alone late at night, crying yourself to sleep
I was asked by a number of people after my ACA presentation, where did my ideas about how to format a presentation? I found the following resources helpful.
Practical Advice Let there be a Stoning (pdf) by Jay H. Lehr which is the best science presentation rant
First, download the paper An Excel Spreadsheet for a One-Dimensional Fourier Map in X-ray Crystallography, by William Cleg. There is a spreadsheet under the supplement section you may want to download so you can play along (see picture below).
I had to adjust the security level in Excel in order for the macros to run (Tools -> Marcos -> Security).
I also had to restart Excel in order for the change to take effect.
1) Scroll right and you will see the labels for the first 13 rows (under W).
The Bragg reflections are listed in the first row
The phases are listed in row 3 (highlighted).
The first exercise uses a reduction in calculating the 3D fourier transformation to 1D. So, instead of ‘hkl’ you will just see ‘l’ written (see equations at the left of page 909).
Note: l=0, which is the total number of electrons in the unit cell and, therefore, the sum of all other reflections
As you toggle on and off ‘Use Correct Phases’ and ‘Random Phases’, you will see row 3 adjusting (highlighted) as well as your graph updating
Notice how the fourier synthesis is affected by these adjustments.
Now, suppose you don’t know the phases (like in the random case). How would you get to the ‘correct phases’?
We cannot simply guess the signs since there are 2^21 combinations (2 since, in this case, the phase can only be -1 or +1; and 21 because that is the number of Bragg reflections measured).
This presents a problem. These signs are not measured directly and there are, literally, millions of possibilities to generate the correct fourier synthesis. You can imagine how the problem becomes more complicated when you are dealing with 3 dimensions and thousands of atoms.
