P212121

As promised, I will be posting the main points from my presentation at the American Crystallography Association meeting this year.

Can we improve the way we currently communicate online?

Let’s take a look at how we are currently communicating with each other online. If we have a question about Pymol, we have to sign up for the Pymol bulletin board. If we have a question about Phenix, we have to sign up for the Phenix bulletin board. If we have a question about CCP4, you guessed it; we have to sign up for the CCP4 bulletin board.

The system is currently set up with the program developers in mind. The developers have the community coming to them. Why? Because it is more convenient for them. If you have a question, you seek them out.

Unfortunately, that means you’re going to have to join multiple bulletin boards and get bombarded with spam. It’s crazy what you’ll find in your inbox! Job postings, equipment for sale, auto-response emails letting you know that someone is out of town. Just this month there was even a phishing scam on the CCP4 bulletin board! I think you’ll agree the system needs to be improved.

In an effort to change the way we currently communicate online, I turned to blogging. For those of you who are unfamiliar with blogs, they are a great alternative to bulletin boards. They eliminate spam because they’re not email based. The discussions can be organized by categories and tags so you won’t have to scroll through tons of threads. A blog can also serve as a mutual site for users and developers to come together and interact.

What do you like about the email based bullentin boards? Do you feel there is a place for forums and blogs?

Part 2

A new poll has been posted to the right: How long have you been using crystallography in your research? If you would like to expand on your answer, feel free to comment below.

I get a lot of junk mail. As a result, I end up spending a part of each day reading these emails only to discover they’re spam and need to be deleted. I find that a lot of this spam is related to crystallography. Most of these emails tend to use my first and middle name in an attempt to appear more personal. Many of my good friends don’t even know my middle name so, naturally, I wondered how these companies were able to attain not only that information, but my email address as well.

If you just take a look around, as I did, you’ll be able to connect the dots (ACA email list rates (pdf))

The ACA is selling your personal information to various companies and organizations.

True, they’re not breaking any rules in choosing to do this, but every time I am sent an email from one of these companies, I lose a little respect for them. Mainly, because it is clear that they are not respecting my time.

Surely, a company needs to advertise but sending out spam to everyone is not the way to do it. If you don’t believe me then maybe Seth will be able to convince you.

What to do?

1) Make the email personal: “I really liked your blog post on XYZ and thought you might be interested in…” (make an effort)

2) Engage, contribute, interact. I don’t know Peter from Emerald Biosystems, but would love to meet him. The company engages the community (is attending ACA this year), contributes (via their own blog) and interacts (writes thoughtful comments)

Despite your best efforts…


…its still spam.

How is one supposed to know if they have receive this message in error?

Sadly, the only suggestion I’m given to fix this is to waste more of my time. I have to write them a blog post email asking them to stop sending me mail I never asked for in the first place.

Note: I won’t be buying your used Rigaku machine but it’s nice to see you’ve kept your options open (here, here, here, here, here, here, here).

Over the last 6 weeks, I’ve been running a poll here on P212121 that asks people whether we need an X-ray diffraction image data bank. The results are in! The vast majority of voters believe we do, in fact, need a image data bank and that it should be free.

Final Results:

Do we need an X-ray Diffraction Image Data Bank?

• Yes, free access (79.0%, 78 Votes)
• No, need to store images (13.0%, 13 Votes)
• Yes, pay for access (5.0%, 5 Votes)
• No opinion (3.0%, 3 Votes)

Total Voters: 99

One of the biggest benefits of the poll was one user’s mention of TARDIS in the comments section. I was able to attain more information about TARDIS and it looks like it will satisfy our need!

You can do this by using Coot and a simple text editor. This can be helpful in preparing figures that discuss biological function. The steps are as follows:

1) Display the symmetry related molecules:
Draw -> Cell & Symmetry…
Note: I changed the master switch to ‘Yes’, adjusted the radius to 50, and then hit ‘Apply’

Below is an overview of the crystal packing:

2) Attain a perspective that will allow you to easily click on your desired symmetry molecule. Below is a zoomed in view of that same packing.

3) File -> Save Symmetry Coordinates
Your pointer will become a small cross shape. Now, click on your desired symmetry molecule.

4) Give the file a name you can remember for at least 15 seconds:

5) Open your original pdb file and then newly generated symmetry pdb files in a simple text editor. I am using gedit on a linux machine in this example.

6) Rename the newly created pdb file from ‘chain A’ to ‘chain B’.
Note: If you do not rename the chains, the atoms may create strange connectivity such as long distance disulphide bonds in cysteines.

Important: I have an ” A ” (there is a space on either side of the A). I always scroll through the pdb file to make sure I’m not replacing the letter A in an undesired place. For example, if you simply replace “A” you will mess up all your CA (carbon alphas) and residues abbreviations such as VAL.

7) Copy and paste ‘chain B’ into your original pdb file. You should copy/paste the ‘ATOM’ section and leave out the header (everything above the ATOM section) and the END (it is at the bottom of your pdb file).

Rename the file and save using ‘Save As’. This way you will have the original monomer available should you need it in the future. If you accidentally overwrite the original, you can always just delete the second chain and re-save the file.

9) Display your newly created pdb file and make sure that your new pdb file is correct.

I have been able to get some details about TARDIS, which was mentioned in the comments of the post:Do we need an X-ray Diffraction Image Data Bank?.


A number of tools for TARDIS are coming online in the near future. The tools are being designed so that labs can install the repository software at no cost on a basic PC server that will allow the deposition of images with minimal annotation (5 or 6 lines of text describing the experiment).

If your server is on their network, TARDIS will be able to locate your data and make it available to everyone. They are open to having anyone who wants to deposit images before the tools are released to contact them and they will deposit the images on the server for you. I have been told that the tools are going to be lightweight and easy solution to the problem. I am looking forward to their release!

Although not explicitly stated, it looks like the server will be open to anyone in the world that wishes to deposit their images. I have been watching the site for about 6 weeks and have noticed that no new structures have been deposited. I hope that with the release of these deposition tools that the number of data sets will greatly increase.

PDBeMotif is a good way to search for sites, motifs and ligand interactions with a given PDB file.


Use the ‘Upload PDB file’ to search the protein data bank for structures.


You can then upload your PDB into the server for searching.

Note: the structure that you are searching with does not need to be in protein data bank.

In addition, you can use SPASM structural motif hunter– either download or run it from a server. SPASM uses a max of 500 atoms so you will probably need to edit your PDB file for the specific motif that you are searching with. If you want more information about SPASM then click here.

If you are in need of a lighter perspective this Monday then you may want to check out NCBI ROFL.

This site is run by a couple of UC Berkley graduate students that have been able to track down various scientific articles with amusing subject matter (some more than others).

I am tempted to put a warning that the site’s contents may not be professional, but then again, it is my fellow scientists that are responsible for generating these articles. Wonder if they are getting a lot of funding…

The next step in science journals is online. In recent Nature news article, “the American Chemical Society (ACS) is taking steps towards turning most of its academic journals into online-only publications.”

I along with others have been expecting that science journals would move to an online format. I have been following the comments of other blogs that have discussed various aspects of the issue. The comments have been quite fascinating such as those from Farewell to Hard Copies at the blog In the Pipeline. A number of comments, from that post as well as the correspondence to Nature indicates that not everyone is going to happy with the change.

My guess is that the reasons mentioned are not going to convince the ACS to change its mind (assuming the rumor is true). If you are uncomfortable with the idea of having scientific journals online then here are some tools to hopefully make the experience less stressful.

1) How to find scientific articles
If you are simply using Google scholar or PubMed then you are missing out.
-I have already written about hubmed.org
These FireFox plugins are worth looking at Eccellio Science and i-cite

2) Taking Notes
Mac: Skim PDF Reader and Note-taker for OS X
Windows: Adobe Acrobat Full Version (not just the reader)
Another choice: PDFpen you could use the demo until it runs out.

2) Highlighting
Firefox add on: Wired-Marker (for Firefox 3.5 click here)
Highlight text then drag to a folder to display your desired color (tutorial can be found here)

3) How to quickly and easily track multiple websites
RSS feed reader

4) Difficulty reading a Computer Monitor
Firefox add on: NoSquint (version for Firefox 3.5 here)
This add on is helpful because it allows you to hold down the ‘ctrl’ key and then use the mouse to scroll and adjust image and text size.

5) Quickly viewing PDF files
Mac Users: Firefox PDF Plugin for Mac OS X
Window Users: PDF Download

6) Serendipitous discovery
I use Google Alert for certain key words that may relate to your research. For example, crystallography or phosphotransferase.
-If your word appears in any news stories then you will be sent an email with an excerpt and link to the article

Finally, I would like to acknowledge a great post over at Bitesize Bio that discussed the Firefox add-ons mentioned.

If you are a mac user then the program Papers may be worth checking out.

RSS stands for Really Simple Syndication.

Problem: You are trying to track multiple web pages at the same time by bookmarking them. This is inconvenient for the following reasons:

1) The site may not have updated since the last time you checked, causing you to waste time by viewing information that you have already seen.
2) If a site updates quite often then you can miss out on information, if you do not check the site enough.

Solution: Get a RSS reader

1) Go to Google Reader (there are others, but this works fine)
2) Click on ‘Create an account’ (unless you already have an account with Google then just sign in) then fill out and read all pertinent information
3) Next click on ‘Add a subscription’ located in the upper left

4) Type in www.P212121.com
5) Now you can enter all other worthy websites!