P212121

If you are a fan of neutron crystallography then you can appreciate the importance of crystal size. The reason we need large crystals for neutron diffraction is that neutron sources produce far lower fluxes than that of X-rays. Despite optimism about crystal size being reduced to ~0.1 to 0.3 mm^3 when the macromolecular beam line is running at Oak Ridge National Lab, crystal size is currently a critical factor.

The problem of cutting crystals down to size seems preferable to trying to grow them twice as large. A recent paper by Matsumura, et al. proposes a ‘new’ crystallization method utilizing the properties of semi-solid agarose gel at a concentration of 2.0 % (w/v). The paper takes the challenge of growing large crystals head on and is worth a look if you are considering neutron crystallography.

As more crystals undergo neutron crystallography it will be interesting to see the how crystal volume and perdueteration play role in data collection. Is a 90 % perdeuterated protein with a size of 0.3 mm^3 better than a 0.5 mm^3 crystal exchanged against deuterium for a month? I see a lot of exchangeable hydrogen counting in order to answer this question. The unit cell volume would also need to be considered. Oh and for those that like random shout outs – it was great seeing everyone at the Ohio Valley Crystallography Conference this weekend!

If you are looking for a way to view structural interactions in 2D then MONSTER is definitely worth checking out. The clean site design results in a very intuitive user experience.

You can generate a 2D map by uploading a PDB file or by using an existing PDB id (click load). The site states that it can take from 5 to 30 minutes to generate an output (3 to 11 minutes for my submissions). An email is sent once your data has been processed that includes a handy hyperlink.

The 2D or 3D structure can be viewed for each interaction. If you are looking for an interaction within a chain then you would need to divide the chain and rename it. The total buried surface area is also generated.

The java based output can be adjusted in real time. For example at the bottom of the window, the min and max distance for interactions can be adjusted. The bond type is color coded between residues although is a bit a hard to see. Overall, MONSTER certainly is a handy tool for presenting and exploring interactions.

I can talk for hours about how ordering chemicals can be made better. As much as I like talking about the problems, it is more fun trying to fixing them.

Don’t Compete on Price
I had employees from another company tell me that competing on price is a bad idea. The idea is that if companies compete on price then it is a race to zero. Funny, how these same companies are selling TCEP for more than 5 times our price.

I can think of low cost providers of cars, food, clothes, but who is it for research supplies? I get frustrated watching my neighbors spend a year putting together a local 5k fun run for cancer research knowing that it is gone in two bottles of IPTG.

Value
The problem with competing on price is that quality can suffer. The great part about chemicals is that the contents and purity are right on the bottle. Value can show up in other areas such as customer service, which if you ever have a problem send me an email sean < @ > p212121.com and we will get it sorted out. As a side note, by being a small company (no meetings, no TPS reports) it is great getting customer feedback and implementing it within hours.

Sales representatives can certainly add value especially in instrumentation, but for most of our products you don’t need to be told to add water. Interrupting my day to drop off of piece paper or a catalog is not a good reason to double the price.

Hidden Pricing
Many companies don’t even show their prices on their website, fliers or catalogs. The idea is to take advantage of an uneducated customer base. If customers don’t know what a fair price is then it is easy to overcharge. A couple of approaches to keep scientists from shopping around is to offer new lab discounts with the idea that you will simply reorder at a higher price point. Another method is to mark up prices then hand out 20 percent off discounts making customers feel like they are getting a special deal.

The cost of shipping is often hidden, which can turn a good deal into a bad one. I don’t know of any other industry that allows customers to purchase items and then be charged an unknown shipping price after the item is sent.

Selection
Especially, for crystallography labs, where can you buy kanamycin, detergents and crystal mounts? We have a long way to go, but we are working on it. Contact us if we don’t carry an item and if we can’t list it then we will do our best to send you a competitor that does. We now have access to thousands of items that we are in the process of adding so we maybe to add an item in minutes. The P212121 store just doubled in size again and now offers more than 200 products.

Being scientists, we may have to work on our marketing skills (imagine saying P212121 all day). We just realized that we are supposed make a press release every time we add another brand. At the moment, we have more important work such as returning customer emails, adding products, page redesigns, updating the search function, etc… I hope you don’t mind.

Last month, I was talking with two sales reps about selling online. They told me that scientists do not buy from companies they haven’t met. I wonder if that was the argument used by sales reps when they sold vacuum cleaners door to door. The vast majority of our customers I haven’t met in person, which is great. This reduces our need to hire, pay for travel and buying those rolly bags, which help keeps to keep our prices down. We may be wrong and things don’t need to change, but so far so the response has been great, which of course wouldn’t be possible without you. Thanks as always for your support.

If you are studying RNA-protein interactions the RNA-Binding Protein DataBase (RBPDB) is worth a look. RPBDB contains 1453 in vitro and in vivo experiments, 272 RNA binding proteins that are divided into 71 motifs. The database is broken can be searched either by your desired protein or RNA. The experimental data contains a variety of binding data including ITC, NMR, gel shift assays, fluorescence and more (see the paper for a complete list).

If you come across a result you are interested in then you can simply click on the PubMedID which is linked to the respective article.

Enjoy.

If you are looking to create a disulfide bond (who isn’t?) and want to have an idea of which residues to mutate check out SSBOND. SSBOND will take an existing PDB file and predict which pair of residues (that if mutated to cysteine) would form a disulfide bond. To use SSBOND simply upload your PDB or you can download the program. Here is a clip from the output for text:


As always, if you use SSBOND don’t forget to reference it.

A reader points us to a PLOS article that examines high impact paper citation trends. (A separate issue is whether high impact journals produce the best science.) The paper examines which of the following three hypotheses are supported by their findings.

1) Newton: to see further only by standing on the shoulders of giants
2) Ortega: top-level research cannot be successful without a mass of medium researchers
3) Ecclesiastes: scientific advancements can be considered as the result of chance processes

The paper concludes:
“…the higher a paper’s citation impact the stronger it is connected to preceding high-impact research…”

The implication toward scientific funding is also addressed:
“Our findings raise the issue of whether limited resources might best be concentrated in support of those scholars (research groups or institutions) who have already contributed to the literature by publishing high-impact papers (belonging to the 99th percentile rank class). A concentration of resources on these elite structures seems to be practical especially for the life sciences and health sciences.” (emphasis mine)

Do you think we should put more (or maintain?) funding towards those publishing at the elite level?

We discussed the need for a simple tool that would allow for the quick extraction of an amino acid sequence from a PDB. @TommyCarstensen was kind enough to create that tool.


To use SEQRES2FASTA simply copy/paste the amino acid section from your desired PDB into the text field. Alternatively and perhaps more direct, you can input your desired PDB ID into the second input location. There are certainly a number of ways to extract this information (PDB Goodies comes to mind), but none that are this simple and direct. Thanks again, Tommy.

Giving a talk or a poster is a challenge because you are presenting answers. The complimentary skill is asking questions.

Asking relevant questions can be done after any talk or poster. The opportunity for asking questions far exceeds that of presenting. If you can ask thoughtful questions then you can add value far more often.

Perhaps instead of thinking about what you can present, think about what you can ask.