P212121

Mac users sometimes get the short end of the stick when it comes to scientific programs. So for the Mac users in the crowd, I thought I would mention a program that is only for MacOS10.4 or higher. XPlasMap is a DNA mapping program that allows you to generate circular (plasmid) or linear DNA maps.

The program could be quite useful for generating maps for publications or presentations. XPlasMap allows you to easily highlight restriction enzyme cut sites, antibiotic resistance, open reading frame locations, tags, introns/exons, etc… The DNA maps can be imported from GenBank or FastA file. The user guide is included in the initial download and is full of screen shots that are really helpful.

Scientists love to make plans.

Scientists are often asked to make 2-5 year plans from dissertations as graduate students to grant applications as professors. The problem with long term planning is that it is guessing. Sure, having a since of direction and reasonable expectations is important, but the activity itself of creating a multiple-year-long-term-plan is time wasted.

We can’t predict or control the future of funding renewals or being scooped. A long term plan serves as a guide when you have the least amount of information. A long term plan can creates stress, if we don’t realize it was a guess in the first place.

Instead of planning for the next 5 years, plan for this month or week or better yet, how about for the next 30 minutes. By allowing immediate results to determine the next step, we can progress more rapidly.

There are two websites that you may not have heard of called Google Twitter and Facebook.


For some it maybe better to connect here on the blog and for others it maybe Twitter or Facebook. If it is either of those two other sites, let us know so we can hang out.

As a bonus, you can also connect with each other!

PDB Goodies is a web base program that allows you to quickly edit PDB files. The program can generate the following outputs:

• Removes user specified range of residues from the given PDB file
• Remove HETATM(s)
• Renumber the residues
• Display amino acid composition, molecular weight & volume
• Calculate average temperature factor
• Change temperature factor
• Remove hydrogen atoms
• Change the residues to poly-ALA
• Pick atoms within a specified temperature factor
• Convert orthogonal to fractional coordinates (was looking for a this function when I found this program)
• Calculate bond lengths, bond angles & torsion angles
• Change occupancy
• Change chain identifiers
• Convert PBD to Fasta format and more!

These operations can be done through other programs such as Coot and/or the PDB Editor.  The benefit of using PDB Goodies is that it is simple (no digging for functions) and web based allowing it to be use across all operating systems.  I mean seriously, who doesn’t like goodies?

Wow. We’ve covered a good number of programs, databases and servers here on P212121, but I still get blown away by the great work researchers are putting out. We recently talked about the crystallization of protein-DNA complexes and wanted to follow up with a great database for those that are looking for structural information. The PDidb (Protein-DNA Interface Database) really owns the protein-DNA database landscape (if you are looking for others see the section in our crystallography programs list). So what makes this database special?

Inputs, the database contains 922 entries (they use a 2.5 A cut off from the structures in the PDB) that can be filtered extensively such as by whether the DNA strands have sticky ends, classifications based on interactions and of course simply using the PDB ID.

The database also has a statistics page with pie graphs that are click-able so that you can easily view the structures in that particular category.

The output is sweet. The upper left panel generates the PDB in JMol so that you can instantly examine the structure. The main panel contains various statistics of interest.

Finally and this is really nice if you need to get a presentation together with a simple click (on the pdf symbol below Jmol) – the structure can be outputted using nucplot to show the pertinent interactions.

My only compliant is that the single strand DNA results contain double stranded structures.

…because sometimes you just aren’t sure where your protein is…

Sara over at A Different Wavelength reminds us that it has been a 100 years since Nobel Prize winner Dorothy Hodgkin was born. The post touches on and points to various historical perspectives on Dorothy.

When I think about the history of Britain and the Nobel Prize, the discovery of the structure of DNA comes to mind. I imagine those that read this blog know that Watson, Crick and Wilkins received much of the credit of the structure of DNA. Rosalind Franklin passed away before the Nobel Prize was issued resulting in her being less well known for her contributions.

I have always had an interest in how this fundamental discovery came about such as how long it took to figure out the structure after having the diffraction pattern? Was there a person that especially critical in the discovery? What was like to work with Crick? How did Watson attain the critical information from Franklin? I have heard presentations by Watson, but have always craved a perspective of a scientist that wasn’t directly involved.

Well, I have been able to line up such an interview. I don’t have an exact date set, however I wanted to give you as much time possible to think of questions and hopefully answers that would interest you about the discovery of DNA. I will update this post with a comment when a date is set (it could be months away) just in case you are sitting on a question and don’t add it right away.

Jena Library of Biological Macromolecules (JenaLib) is an atlas of the Protein Data Bank (PDB) as well as the Nucleic Acid Database (NAD). JenaLib has many options that build upon the PDB and NAD. A feature that jumped out to me was the ability to generate customized lists. I have been using the PDB to generate customized lists by exporting them into excel followed by various sorting tricks.
The process has some friction.

JenaLib under Entry Lists allows you to create customized lists on a variety of topics:

These can be further refined by a number of factors such as collection method, Ligand/Ion and much more. The list can be outputted as html or a .tsv file. A TVS formatted file can be imported into excel via Edit -> Paste Special -> Unicode Text. If you use this import method then each output will be assigned its own cell.

I could see this being really helpful for those that are involved in the bioinformatic side of macromolecular structures.

We aren’t going to be experts in everything therefore we have to choose: breadth vs. depth of knowledge. Breadth means that you have an awareness of subjects that extend across different areas. Depth is being an expert in one particular area.

Breadth allows you to see connections between topics. The value can be in setting up collaboration among scientists in different fields to answer a question. Breadth is useful in seeing that a problem may have been addressed in another area. If you have an area of expertise then adding breadth is important.

Depth is being on the edge. Depth makes you the go to person if someone has a question on a subject. If a colleague needs a particular skill set for a research grant, they come to you.

Make sure you have depth. Breadth is tempting since you only need to read a couple of review articles to have an opinion. Depth takes time, depth is a struggle. If you don’t have an area of expertise then it becomes hard for people to find you. People find you when you are on the edge. Are people searching for you?

A critical component in crystallography is the generation of an electron density map. The electron density map is important since it guides the creation of the protein model.

An equation for the calculation of the electron density (ρ(x,y,z)) is as follows:


Fhkl is the amplitude of the wave which is proportional to the square root of the intensity – this is measured during the crystallographic experiment as a reflection (or spot)
all hkl represent the measured location of the reflection on the detector
Vc represents the crystal volume
α is the phase

The diffraction pattern is collected with the spot positions and intensities being recorded. The intensity of the spots allow for the calculation of the amplitude. The volume of the crystal (Vc) can be determined from the spacing of the reflections. The component that is not recorded during crystallographic data collection is the phase (α).

Since the phase is not recorded it creates a problem hence the name “the phase problem” in crystallography. The challenge is to reconstruct the electron density map by approximating phases.