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The Outline Slide is a staple in scientific presentations.


The Outline Slide presents the audience with the path that your presentation will follow. The slide provides the first step in a three pronged approach of giving a presentation, “say what you are going to say, say it and say what you’ve said.” This approach reinforces the main points of the presentation to your audience.

How about instead just “say it.”

How about get to the point, tell your story, people don’t leave presentations saying, “great talk, wish it was longer.”

If you are worried that by not giving an Outline Slide that your talk will be hard to follow, you are probably right. However, the Outline Slide isn’t the problem, it is the rest of your talk.

The following will allow you to create a 2Fo-Fc map using CCP4 from a mtz file to be displayed in PyMOL.

1) Start CCP4i, select ‘FFT‘ from the program list or ‘Run FFT – Create Map’ under the Map & Mask Utilities

2) This map will cover all the atoms in the PDB therefore must be changed (see red arrow). The F1 and PHI have also been changed from the default (see red circle) – RUN
Note: if you would like to calculate a Fo-Fc map use DELFWT and PHDELWT respectively.

3) Change the ending of the new map file to .ccp4 (can be either abc.map.ccp4 or abc.ccp4, but not abc.map)
4) Load the map into PyMol select ‘A’, mesh, 1 sigma level and the electron density should appear

If needed, here is a previous post that will show you how to move from this point closer to a publication quality figure (also checkout the PyMOL wiki).

The list contains 250+ programs, databases and servers so if you are searching for a crystallography related program then there is a good chance you will find it here. If you notice a program that is missing or an update, feel free to leave a comment.

The Murthy retraction fun happened about six months ago. Cell still hasn’t (are they ever?) retracted the 2001 paper, Crystal Structure of a Complement Control Protein that Regulates Both Pathways of Complement Activation and Binds Heparan Sulfate Proteoglycans, which is based on the two retracted structures 1G40 and 1G44.

The problem with not retracting the paper is that researchers could end up citing this work. Their resulting papers could then be cited by others. The problem scales.

For example:
The 2001 Cell paper is cited by Murthy in his 2003 paper, Biochimica et Biophysica Acta, which he then cites in 2009 in The Open Biochemistry Journal after the retractions were announced.

Just a crazy idea: why not retract all the papers that are based on these retracted structures?

PS> Have you ever looked at the Murthy structures that were not retracted (1AY1, 1BGX, 1HEF, 1HEG, 1SBG, 1HPS and 1HOS)? They all have the suspect time line, but one in particular looks quite strange.

If you would like to practice your symmetry or view a structure from the PDB, ‘There’s an App for that…’

The app Crystallography allows users to draw up to 17 planar symmetry groups. The app deals with the concepts of planar groups, Hermann-Mauguin symbols, symmetry operations, asymmetric unit, general and special positions.



The application has resulted in a publication in the Journal of Applied Crystallography. Once you are done with your drawing you can submit it to be posted in the online gallery.

Although you can’t yet solve your structures on your phone, you can look them. The app Molecules has recently been updated and is now compatible with the iPad.

Molecules allows you to view rendered structural images from the PDB.

I will look forward to following what other applications related to crystallography find themselves on mobile devices. I have a hard time imagining solving a structure on an iphone. Would you use your phone for crystallography? What crystallography applications would you like to see on mobile devices?

I wrote awhile back about lab organization and thought an example would be helpful. We had an undergraduate working in our lab write up this protocol to help future students. The result has been a couple pages that have saved days of time for our current students.

The protocol will vary depending on the protein, lab set up and will need to be updated overtime. If you want to copy this protocol and tweak it to fit your situation, feel free.

Does your lab have something like this in place?

As we all know, Acta F is the Nature of data collection. In a moment of weakness, a number of collegeus decided my contributions were worthy of authorship. If you are into hemoglobin and neutron crystallography this paper (pdf) is for you.

You don’t need E. coli, if you can get your hands on buckets of protein.

Here are some lessons that were reaffirmed while working on the project:

1) Focus
We only had a couple of months to finish the project. Everyone that was involved knew the time line since it was dependent on available beam time. The result was reduced thrashing.

2) Teamwork
I have been working independently on most projects. I mean this in the sense of lab work. I am fortunate to find myself surrounded by great people to bounce ideas off of. In this project, the tasks were divided, which exponentially increased the speed. For example, a person would be running a column while the another is setting up crystal trays.

3) Always Learning
Hemoglobin has a long history and is probably one of the most studied proteins to date. The R/T transition states is often covered in introductory biochem courses. The part you may have not of heard is that there are other states such as the B state (pdf).

I have edited my fair share of PDB files to attain the sequence for an alignment. If you are looking for a simple way to extract the protein sequence from a PDB file then check out the utility tool called ‘Make sequence file from PDB file‘ at the WHAT IF server. The tool/server was on the slow side in my hands.

Is the server a little slow for you also? Also do you know of a tool that will allow you to submit a number of PDB files and output them as a sequence alignment? That would rule.

Pursuing the crystallization of protein-DNA complexes can wreck your publication rate. I have seen a number of colleagues dedicate years attempting to crystallize protein and DNA complexes, only to be unsuccessful in the end.

Here are a number of tips and tricks I hope you find helpful:

1) Adjust DNA parameters before protein
DNA plays a critical role in crystallization since it is often the source of crystal contacts.

2) Start with 10-11 base pairs of DNA
Increase 1-2 bases at a time, usually stopping at 21 bp. The idea is that a helix forms every 10.5 base pairs and forms a pseudo-continuous helix.

3) Sticky ends
The sticky ends do not have to be complementary. Blunt ends can work, but this would not be one of the first variables to change.

4) Screening
Expect all the normal fun of protein screening. I would favor PEG or MPD in screens (Natrix) rather than high salt screens. The high salt can disrupt the charged interaction between the protein and DNA.

5) Get your DNA from IDT
We have also ordered through GeneArt

6) Run a gel
If you are unsure if you have protein-DNA complex formation

7) Don’t worry about purification
This is assuming your DNA is from a commercial resource (it has already been purified). If you are running out of options, a quick run over a HPLC may help.

8 ) Concentrate your protein-DNA before crystallization trials
If precipitation is occurring, consider running DLS to help determine at what concentrations precipitation is occurring

9) Use a ratio for protein to DNA of 1:1.2-5

10) Cryoprotect your Crystals
If your crystallization condition does not contain a cryoprotectant then try a second pass through one of your favorites, like glycerol or LV Oil.