Many employers list attention to detail as an important aspect of job function.
Just don’t forget about attention to obvious.
The career path in crystallography is hardly straightforward. A scientist can end up moving many times over the course of their career. You know – back breaking, couch up 3 flights of stairs, garage bag full of clothes moving.
There are three main areas that are usually considered when looking for a position: government, academics or industry. A transition between academics to industry maybe the least understood since much of what is done in industry is not made public.
Peter comments:
…I would be extremely grateful if you could start a thread on people’s experience in moving from academia to industry. I am interested in doing this once I’ve finished my post-doc… It would be great to hear stories from people that have made the transition without prior industrial experience.
How does one best prepare for this type of transitions? Have you made the transition from academics to industry? Could you share some words of wisdom? Thanks.
We have a page dedicated to tools used in macromolecular crystallography.
My goal is to provide one location that houses a collection of beneficial tools. Having these programs in one spot will ultimately save everyone a lot of time because it would eliminate endless searching. For a long time, ExPASy has been a great site for tools. Unfortunately, it does not appear to be maintained any longer; many of the links are now broken. ExPASy tended to be repetitive and had a lot of tools that we do not need, like Popitam for mass spectrometry.
I have been updating the Tools page with new content but feel that a number of great programs and online tools are still missing.
What are we missing? Should data processing and refinement programs be included (ie. ccp4, cns)? What tools have you been using that are not listed? Could the ‘Tools’ page layout be improved? We need one great location for crystallography tools, can you help?
Crystal! Sweet.
The next step is to determine whether the crystal is comprised of salt or protein. Here is a list of methods to help you determine whether you are dealing with a salt or protein crystal.
1) Prediction Tools - can be used to determine if the drop components have the possibility of forming a salt crystal.
2) Birefringence – is a sign of salt crystals although it is not visible in protein crystals that are cubic. A set of polarized lens are needed to check for to see if the crystals are birefringent.
Look for salt crystals to have strong birefringence while proteins are weaker
3) Dyes - such as methylene blue are able to enter large solvent channels of proteins that are not present in salt crystals
Look for dye to be absorbed into the protein crystals and not salt
4) Dehydrate - by removing the crystal from the drop.
Look for salt crystal to maintain its structure while protein to turn to mush
5) Crush - the crystals using a small tool. Protein crystals are softer than salt crystals due to their crystal packing. It is helpful to try this technique with a number of known samples to gain experience. Tip: Wick away excess solvent to save time
Look for protein crystals to collapse when compared to that of salt
6) Glutaraldehyde - can be added to your drops (~1 %), if protein is present the drops will turn a yellowish color. Since glutaraldehyde is quite volatile it may also be added to the reservoir, if you decide to go this route then use ~2 % concentration. Any free amines will turn yellowish so watch out for the presence of other protein or components in your buffer such as TRIS.
Look for a protein crystal to turn a yellowish color
7) SDS-PAGE - can be used by dissolving your crystal (or the entire drop)
Look for: the correct electrophoretic pattern
Control experiment - can be done (this is science) by setting up the exact same condition without your protein.
Look for motivation
9) Crystal shape - alone can be very misleading between salt and protein crystals. However, I have noticed the wings of death crystals (magnesium phosphate, in this case) appear quite distinct.
Look for wings of death
10) X-ray diffraction - although obvious, it is not possible for everyone. If you have easy access then this is the only definitive method out of all the methods mentioned.
Look for salt crystals have fewer reflections (larger lunes) compared to protein crystals
A group of scientists have a meeting that results in setting up a collaboration.
The excitement is high.
The next series of events will be easy.
A paper to find.
An email to send.
Next
A reference to find.
A sequence to order.
Followed by:
A post doc assigned to get the ball rolling.
A grad student that learns along the way.
A set back.
It should be easy.
The 3 weeks are now 2 months.
Money has been spent.
Post doc is moving on
Student is near graduating
Something must work! What do we do?
How can we salvage a paper from this work?
What results do we need for this grant?
We need to have a meeting.
Coming up with projects is easy. Setting up collaborations is easy.
Trash at the beginning
How long will this project take?
Who will be responsible for which results?
When are the results to be expected?
What is the plan, if the results are poor?
What will the first paper include?
What journals accept this type of research?
How many papers should we expect?
How does this help our next proposal?
When will we move on?
Be obsessive about the projects you start and committed to finish. Decide now.
Result: By knowing exactly what the project entails, you will reduce distractions.
Inspired by Seth.
The PDB can be pretty intimidating when it comes to extracting information. I still have issues with its search capabilities, which may lead you to think that generating structural statistics is very hard. Thats where the site PDBeStatistics can be of great help.
How does your structure compare with those already deposited into the PDB?
For example, how does the difference between your Rfactor and Rfree (Rdiff) compare against other structures at the same resolution?
To generate this graph:
1) Under Experiment: Resolution
2) Second parameter: Xtal: Rdiff
3) Click on desired area: In this case it is a resolution of 2.5 (currently 807 structures, highlighted in magenta). The Rdiff is displayed along the right hand side, in this case 0.035
You can adjust the range displayed using the slider in ‘Truncate Graph’ (center of graph in blue)
Here is another example displaying the percent solvent distribution across the PDB:
This site can also serve as an excellent resource for presentations. Hey, had to do it 
Thanks to Tom for developing this site and bringing it to our attention.
Sili has been leaving some great comments about his struggle to find a job in crystallography. Sili’s struggle reminds of me of my own introduction to crystallography. Lets just say I can relate.
I used to swim on the USA national team but, unfortunately, it did not pay the bills. I worked a whole string of minimum wage jobs from giving swim lessons to cleaning toilets. I worked 3 jobs at once and trained 35 hours each week. I was pretty busy. 
I ended up deciding to apply for a position at Los Alamos National Lab in genomics since I had a background in biology. After a number of interviews, I was offered the position and was excited for the change of scenery. My lease was up in about 6 weeks so I didn’t move right away. I notified my employer that I would be moving on.
I took a week off between the transition to visit my family and, while there, received a phone call from the person who had hired me. They no longer had the position. Yes, I had the offer in writing (twice, actually), but they simply were over budget and apologized for the inconvenience. So there I was with no job and no place to live. I decided to do the rational thing and drove nearly 1500 miles from Seattle to Los Alamos with everything I owned in my car.
I interviewed with anyone that would see me. It didn’t matter what kind of research they did. I was interested and willing to learn. After two weeks and 15 interviews, I finally had two job offers. One was in a crystallography lab. I was hooked after seeing those macromolecules spin around in Coot.
The message I’m trying to relay through this story is this: if you have the motivation and the perseverance, something WILL work out in your favor. So Sili, hang in there and if your passion is in crystallography – go for it.
For others, how did you first come across crystallography and decide that it was an area you were interested in?
Keeping up on literature can be time consuming. How about having all(?) the structural journals delivered to you? Sounds good. If you do not use RSS then you are missing out. I wrote about how to set up a RSS reader – it is easy.
Here is a list of 17 36 Structural Journals with RSS. I have aggregated the RSS links of the following journals and, as a bonus, added this blog!
The following journals are included
Bonus (ie. someone was kind enough to suggest them)
Here is a link:
http://bit.ly/20EyHw
If you would like to add the entire list simply copy-paste the url into your reader. This aggregated feed has also been set up to have the most recent items displayed first.
Advanced: I entitled this aggregated feed as Structural Journals in yahoo pipes and made it publicly available, if you would like to tweak it (add or remove a journal, filter by keywords, etc..).
Hope that helps.
I have tried this method on 4 different structures and so far it has dropped both the Rfree and Rwork by about 1 percent, but your mileage will vary. For better or worse, one can end up spending a great deal of time trying to lower their R values. I wanted to share with you the steps of how I have been able to drop these values.
1) Complete your structure
-have it to the point that you would submit it to the PDB (maintain your Rfree)
2) Go back to the point in refinement that you were satisfied with the protein structure before adding solvent
3) Add all your solvent from your final structure
-paste them into the pdb file
4) Refine as normal
Your mileage will vary based on:
Crystal packing
Resolution
[add your own here]
Give this a try and drop me a line with your results.
Unless you have been living in a box, you have heard that the 2009 Nobel Prize for Chemistry was awarded for studies relating to the structure and function of the ribosome.
The winners: Ada Yonath, Thomas (Tom) Steitz and Venkatraman (Vanki) Ramakrishnan
The Nobel Prize allows for a maximum of three laureates, but did the Royal Swedish Academy of Sciences get it right?
If you have not heard of Harry Noller, he was the first to propose that the ribosome is comprised of RNA. In addition to decades of devoted research, he also published extensively on the topic.
As reported by the NewsDaily.com:
Dr. Jeremy Berg, director of the NIH’s National Institute of General Medical Sciences, stated that “One of the reasons people have been unsure of the ribosome structure as a Nobel prize is that getting down to three people is tricky. Harry Noller of the University of California Santa Cruz has been one of the real leaders of sorting out the biochemistry of the ribosome for a long time.”
Professor Dana Carroll, who hired winner Venkatraman at the Univeristy of Utah was reported to believe that Harry Noller… should share a piece of the honor for his work in ribosome function.
The response across twitter was heartfelt:
The facebook page containing nearly 100 members dedicated to Harry’s Nobel Prize run was devastated.
Harry has been humble saying, “I’ve gotten more recognition than I deserve.”
I have started a new poll (to the right), feel free to give it a click.
What do you think? Is Harry the Rosalind Franklin of the 21st century?
[Results]