P212121

PDB Structure Quality is a website that separates variables that are often correlated during crystallographic data processing and refinement. The paper entitled, Quality of protein crystal structures, is quite good and brings to light a couple of interesting points 1) the higher the impact factor of the journal the lower the quality of structures and 2) PDB quality has not significantly changed over time. If a macromolecular structure at given resolution was deposited in 1997, it is comparable to one published in 2007.

The database is current as of Nov 17, 2008, so the most recent structures will not be present.

As a heads up, the paper and website are not the same (as stated on their website):
Note: The number of independent and dependent variables has been expanded in this analysis compared to the published literature. Independent variables describing the crystal have been mined from the available structures. Those variables that were missing have been multiply imputed.

The site also has a PDB Structure Quality prediction tool to calculate the R-factor, R-free, the occupancy-weighted B-value, and the ramachandran violation percentage. As stated on their site, “This task allows a crystallographer to determine what validation metrics they should obtain at the end of refinement. If the refined validation metrics are not as good as those predicted, then further model building and refinement may be warranted.” Sweet.

I have been working with a protein that is quite soluble in sodium potassium phosphate (yes, I should find another buffer). I set up crystal trays using screens from each of the major of screen manufactures: Hampton Research, Qaigen, Microlytic and Emerald Biosystems.

I came across a number of conditions containing magnesium chloride so was worried about the formation of magnesium phosphate crystals instead of protein crystals. I then decided to search for a tool that would allow me to quickly identify what conditions have the ‘possibility’ of forming salt crystals. I came across a site called the crystal screen wizard with a tool called the Salt Crystal Predictor. The tool is very easy to use:

1) select a screen (if it is not listed then you can upload your own)
2) write out the protein buffer condition is present while screening

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In addition, if you do not like flipping through pages of what conditions are in which well for a particular screen, you may also find this tool helpful.

Quick Lookup

1) select a screen 2) condition number –> outputs the condition

I would like if the tool did not send the user to a separate page after clicking submit, but is still a time saver.

I have seriously contemplated gouging my eyes out with knitting needles during a number of boring science presentations. I think we can do better. How about this as a place to start?


“You just have to subtract from 10 to know how much longer, I suck.”


“I can read faster than this bozo can speak.”

1) Download your coordinate file, if applicable (if you are using an existing structure the coordinate file is probably located in the Protein Database).

2) File –> Open, the PDB file

3) The structure should appear

4) Then click on the H and select everything

5) Then click on the S and select cartoon

6) The cartoon of your PDB should now appear

7) When using Pymol for Figures or presentations it is often best to set the background as white
Display –> Background –> White
Note: If you would like a different perspective, rotate the molecule before the next step

Click on Ray button (upper right) in the PyMol Tcl/Tk window

I previously mentioned having trouble downloading the PDB files from the Zhang Server (I-TASSER). I thought it was just me, until I started getting traffic from users searching for “cannot open PDB file I-TASSER”. The problem ended up being how my Firefox browser was set up on one computer verse another. If you are having this problem – here is how to fix it.

When my browser was not set up correctly, I would get the following displayed when clicking on Download Model2 (for example).


Edit–> Preferences –> Applications


Scroll down until you find the file type PDB then change to Save File then click Close


If you are using an older version of Firefox try the following:
Edit–> Preferences –> Content –> File types Manage

1. Look for a research area that is hot (cancer, green chemistry, energy, nanotechnology)
2. Figure out how to spin your research relates to that area
3. Find a couple of colleagues who each have a specialization (NMR, SPR, Mass Spect., etc…) – cross disciplinary
4. Have each of them write their own section, with the head PI bringing it all together
5. Submit it to a committee that has at least one person you or your colleagues know (or who graduated from the same university).

Below is an overview of the programs that we used during Small Angle X-ray Scattering (SAXS) data processing. This should help clear up how a number of SAXS programs relate to each other (this is not all inclusive).

Overall, I feel like there is some hand waiving in regards to the consistency of the results from the SAXS data processing programs. However, if you cannot attain a crystal of your macromolecule then this biophysical method is probably worth trying.

A quick introduction into what is needed for a SAXS experiment? In addition, you should contact your respective beam line scientist.

The following links are for more detailed information about the programs mentioned above:
Crysol – generates scattering curves from crystal structures
SASREF – rigid body modeling from crysol (see above)
Primus – low resolution data, Guinier plot
IGOR – low resolution data, Guinier plot
GNOM – uses all scattering data as a distrubtion function to determine the shape of the protein
Gasbor – all Q, chain dummy atoms
Dammin – low Q, using dummy atoms
Supcomb – aligns mutiple models to find the most probable
Damaver – aligns mutiple models to find the most probable
Credo/Chadd/Gloopy – model in missing domains

If you end up getting really stuck there is a forum that maybe able to help. Finally, I would like to thank, Jen, for working through these programs.

My favorite crystallography quote has been:

“A structure is worth a thousand gels.” Unknown

I was reading through the comments and came across a quote posted by Rob:

“You gotta set up drops to get crystals.” Larry Shapiro

Do you know any other good crystallography quotes?

If you or your lab has some good ones, please list them in the comment section!

The following is a list of the 27 most popular homology servers, according to Google PageRank .

PageRank 6:
CE – Combinatorial Extension (CE) Method
CPHmodels – Based on profile-profile alignment guided by secondary structure and exposure predictions
SSM – Secondary Structure Matching is an interactive service for comparing protein structures in 3D
SWISS-MODEL – Automated protein structure homology-modeling server
Vast – NCBI’s structure-structure similarity search service

PageRank 5:
BioInfoBank Meta Server – Protein structure and function prediction methods
Dali – Network service for comparing protein structures in 3D
DejaVu – Input to the server is a pdb file with a secondary structure motif
EsyPred3D – Automated homology modeling program
FATCAT – Approach for flexible protein structure comparison
GENO3D – Automatic modeling of protein 3D structure
HHpred – Homology detection & structure prediction by HMM-HMM comparison
HMMSTR – Ab initio prediction of protein structure from sequence
Modeller – homology or comparative modeling of protein three-dimensional structures
Phyre - Protein Homology/analogY Recognition Engine
Rankprop – Ranking algorithm that exploits the global network structure of similarity relationships among proteins in a database
SAM – HMM-based Protein Structure Prediction
TCoffee – Collection of tools for Computing, Evaluating and Manipulating Multiple
THREADER – Protein fold recognition
SWEET – Constructs 3D models of saccharides from their sequences using standard nomenclature.

PageRank 4:
3d-JIGSAW – Automated system to build three-dimensional models for proteins based on homologues of known structure
Consensus Server – Comparative Modeling
FUGUE – Sequence structure homology recognition
HOMCOS – HOmology Modeling of protein COmplex Structure
Promals3D – Alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.

PageRank 3:
What If – PDB file to be used as template, and the aligned sequences of the template and the model.

SDSC1 is currently not operating, but may be in the future

Note: I came across this interesting article comparing the VAST, CE, DALI, DEJAVU and SSM servers.

I mentioned RescueTime and a couple of Firefox short cuts in previous posts. I would like to follow this up with 4 articles discussing how to become more efficient when on your computer.

1 and 2) Check email twice a day and Email Ninja both by Tim Ferriss
-implementing these techniques are not without controversy, but definitely worth considering

3) 12 Firefox Keyboard Shortcuts you will Actually Use by Andy Wibbels
-Before reading this post I was not using ‘ctrl + tab’ to toggle through tabs in Firefox, it is really nice.

4) KeepMeOut Reminds You Get Back to Work by Jason Fitzpatrick
-love the simplicity