I spoke on the last day of the American Crystallography Association meeting this year in Toronto. I missed the first couple of days and, consequently, a lot of vendors. I was, however, able to get in touch with Emerald Biosystems via Twitter (@reducentropy). I was able to set up a crystal card using their new machine called the PlugMaker. I was pretty excited since this was the first time a user sample had been on the instrument.
The machine is neat to watch operate as it combines buffer with precipitant and then injects an air plug to keep each sample separate.
Ok, so this is the lead in for a crazy story.
I am driving home from Toronto when all of a sudden, I am Mr. Popular at customs.
What was the purpose of your trip to Canada?
A science meeting. Are you bringing anything back from the meeting?
Just a protein sample. (referring to the crystal card) What type of sample?
It was at this point that I realized my trip home was going to be longer than expected.
So what to do?
Well, I told him about the sample like a dissertation defense.
I was worried that if I didn’t tell him exactly what the sample was then I might encounter some problems down the road.
So I am in the back of this long line at customs.
All of sudden an announcement comes over the PA system, “Could the person with the biological sample please identify themselves?”
I get brought up to the front of the line and am asked again about the sample.
I, again, explain away.
Blank stare.
I realize this guy has no idea what I’m talking about and that if I don’t make this easy for him then its going to be a long night.
Should I write this down?
Sure.
The customs agent is really nice and prints me off a declaration form about the sample, which I should have had.
I am home for about 4 hours before catching a flight to visit my family in Alaska. I end up leaving my crystal card in my checked bag. So my crystallization experiment gets a couple of doses of about 35,000 ft of pressure change and near freezing temperatures.
A month later, I am on my way back from Alaska and this time, I forget the crystal card completely. So the crystal card gets the pleasure of traveling three weeks in parcel post.
The biological macromolecule crystallization database (BMCD) compiles, crystal data and crystallization conditions from literature. The database is as simple to use as Google. However, I find that I need to use the Advanced search to help narrow down the results. The advanced search options are shown:
I previously wrote about the cryoprotection database (cryo database) and thought it would be interesting to compare them:
Which database is larger?
Cryo:1,777 entries
BMCD: 14,372 entries
Which database extracts the best crystal and crystallization information?
If you are looking for general information about protein crystallization, then the BMCD is by far better. However, the cryo database is helpful if you are looking for that specific information.
An issue I came across when using the cryo database was that it did not list the PDB identification code. This would save users from having to look it up in the original reference. My guess is that the user base of this database is mostly crystallographers so a PDB ID would be helpful.
A point group is a set of symmetry elements that are related to each other about a fixed point. A symmetry element is a point, line or plane around which the symmetry operation is performed. A symmetry operation is the process of transforming into a state indistinguishable from the starting state.
The following link provides a list of the 32 available point groups in Hermann–Mauguin notation. The 32 point groups are generated by performing the symmetry operations listed below:
Note: I am writing the dash over each number as ‘bar’ (how it is pronounced).
Point groups can contain the following operations:
1) Rotation:
Symbol: 1,2,3,4,6
Explanation: The number of times the item repeats in 360 degrees
Example: A three fold requires three rotations to return to its starting position (360 degrees /3; n=3 for a threefold axis)
2) Reflection
Symbol: m or 2bar
Explanation: Created by a reflection across a plane
Example: Place a hand above and below a table with the fingers pointing in the same direction. The table represents the mirror plane while your hands are a mirror image of each other.
3) Inversion
Symbol: 1bar
Explanation: An item is projected through a point that defines a center of symmetry
Example: Put your hands in a separated prayer position, then flip one hand so that your fingers point downward
4) Rotoinversion
Symbol: 3bar, 4bar, 6bar
Explanation: rotate followed by an inversion
Example: Step 1) Think of a fourfold rotation, move to the first position (90 degrees away); Step 2) inversion about the origin
A reflection or an inversion changes the handedness of the molecule and is, therefore, not very common in macromolecular crystallography (most amino acids are L not D in configuration).
If you are unfamiliar with Google Docs then please watch this video:
Here are a number of ways Google Docs can be beneficial, specifically in writing grants.
1) Work Simultaneously: It eliminates the need for people to work on their sections separately and then try to bring those pieces together.
2) Eliminate Version Issues: Eliminates the problem of someone accidentally updating an older version of the grant then having to redo these updates in the most recent version.
3) Simplifies Communication: You can view the document virtually in real time, thus eliminating the need to figure out how far others are on their sections.
4) Comments in margin: Being able to comment in the margins can be helpful, especially if you need a sentence or two from a collaborator in a particular section of the document.
Ok, I am guessing that if you’re still reading this post then you’re not using Google Docs to write grants. This isn’t very hard, but I will type slowly to make sure it comes out clearly.
1) Go to Google Docs and login
2) Create a document (left corner) (New -> Document):a blank document will now appear
3) Go to Share (right corner)
4) Enter the email addresses of those you would like to be able to access to the document. You can also email a link to those you wish to have access. (that’s it)
Some of you may be concerned about having an important document online– is it secure? The following has eased my mind:
1) Is your email better? In other words, are you sure that sticking with email documents is much safer?
2) According to Neil Fraser , an official rep at google, Google stores all of its confidential presentations, documents and spreadsheets online. Neil also makes one suggestion: "When using an unencrypted wireless connection or some other network you don’t really trust, use https://docs.google.com instead of http://docs.google.com. (the difference is the first has an "s" – https vs. http .
I have been searching for a free online resource for crystallographic tables and diagrams. I came across a free Hypertext Book of Crystallographic Space Group Diagrams and Symbols. I am pretty happy about this since an online subscription to the international tables costs thousands.
