Crystallography on the go! Mobile is where the future is at and Molsoft is helping push it along. Molsoft recently released iMolview for the iPhone – now we have discussed mobilecrystallographyapplications on your phone before, however this program has also been designed for the iPad. All this technology for only 99 cents – can’t wait to see what they come up with next!
Here are some amazing screen shots:
Neat video (no sound) of iMolview in action on the iPad:
Feel free to leave your thoughts on how you like the application in the comments.
The Phenix team has been working on producing a great newsletter. The article quality is impressive and makes me again wonder about the long term future of journals.
sc-PDB database annotates more than 8500 binding sites extracted from the PBD. The database would be useful for comparing and predicting how ligands are bound to a particular protein.
Initially, the database uses basic biological Information such as the Uniprot code or protein name. This is then followed up by examining the size, shape or location of the binding site within the protein. Homologous binding sites are then combined and reported.
A recent paper has been published on the database and they have put together a nice how to guide for getting started.
We were able to attain an early copy of the movie Naturally Obsessed and spread the word. For those that haven’t had the chance to watch this great documentary, you’re in for a treat. In my experience, sharing this documentary with friends and family has give them a glimpse and appreciation into what we are doing.
The P212121 store is a 1 year old! The response has been amazing, thank you. The store has undergone a number of redesigns based on your feedback, product search has been improved and product offerings increased (now over 500 items including media and substrates).
The focus of the newsletter will be around new products (what is new, what do you want to see?), conferences (where we will be, where are you going to be?), exclusive deals, contests and giveaways. The newsletter will certainly be unlike any other chemical newsletter that’s around, which we think is a good thing.
We like you, but if for some reason you decide that you are ready to move on – each newsletter has an unsubscribe button. Give the first couple a chance, spread the word if you like it and let us know what you think.
Also for those that don’t like crystals a post on ffAMBER (force field calculations)
Random: We attended our first conference this weekend (GSA meeting in Toledo, OH) and had a blast! What are your favorite conferences? Which conferences will you be attending them this year? I would love to meet up and give out some high fives.
The following is an unedited letter by Dr. Soichi Wakatsuki who is the director of Japan’s Photon Factory, a national synchrotron radiation facility. The letter is a perspective on the magnitude 8.9 earthquake that struck Japan on March 11th. The facility is located about 40 miles north of Tokyo, which is toward to epicenter of the earthquake (depicted as a red square).
***
Dear colleagues,
I would like to express my sincere gratitude to all international colleagues for sending us the warm words and support after the devastating earthquakes which hit the north eastern Japan on Friday March 11th, and the subsequent crisis in the nuclear power plants in Fukushima. This is a national disaster.
I was in a symposium of the Target Protein Research Program of the MEXT (a national project on structural proteomics) in University of Tokyo at the time. 400 to 500 people evacuated the Yasuda Lecture Hall and waited outside for an hour. The University safety official announced that we would soon be able to go back in to the building to resume the meeting, but nobody believed that. Soon after that, we decided to cancel the meeting in the halfway through, and the participants went home, or tried to do so. By that time the traffic in Tokyo and around the country had become a total mess. Without train services, no taxis found, many people walked home 10 to 30 km, or had to stay in train stations or on the road overnight. I myself also had to stay in Tokyo and spent 6 hours to get back to Tsukuba from Tokyo the next day.
The Photon Factory is 60 km north of Tokyo, 200 km from the Fukushima nuclear reactors. There have been no injuries both in the KEK Tsukuba Campus (where the PF is located) and the J-PARC (a new spallation neutron source in Tokai, on the coast) but many damages have been observed. In Tsukuba, we still have very limited emergency power (up to 2 MW), no water, no gas. This makes it very difficult to assess the extent of real damages. On very limited visual inspection, our five protein crystallography beamlines have been spared of major damages, but we need to wait until we turn on the components and bring in the beam. The linear accelerator has seen some substantial damages: three RF components moved by about 10 cm along the beam direction breaking the vacuum, one Q magnet fell onto the floor, some ground water spills. PF and PF-AR rings have seen less of damages: some fallen control racks, but again we need to turn the system on before knowing the real damages.
Several components of VUV-SX bealines have been displaced. All these need to be carefully checked and reinstalled before we can get back to normal operation, which could be, at least, two to three months.
As many of you have seen on the TV, internet, and other news media, the four nuclear reactors in Fukushima, 200 km away from KEK Tsukuba are all in deep trouble. We are really scared by the potential meltdown of any of these reactors. The information released from the Government and the Company are rather limited. I guess they are trying not to scare people but this makes us worry even more. The situation of the nuclear plant has worsened every hour for the last several days, but I do hope that they will contain the damage. At KEK, we are now measuring the radiation level continuously, and so far the highest we have seen in Tsukuba is a sharp rise to 1.1 microSv/h (not really a major health hazard at this level) at 9AM this morning but then it went down to normal. People’s life around Tsukuba is also affected; gas (gasoline) is very scarce and every gas station either has a long queue or closed after selling their stock out. In supermarkets, drinking water, bread, rice, meat, etc. are very hard to find. I have told my children that we are very lucky in that all five of us are together in the house without any major damages,and our extended families are also well, compared to the terriblesituation in northern Japan closer to the epicenters where people lost their lives, houses or loved ones.
We will work together to survive this crisis and try to restore our lives and the science in the coming months, and would very much appreciate your continuous support in these difficult times. For example, I would expect shortage of beamtime during the recovery of the PF and our colleagues at SPring-8 will help us, but would like to ask for your support in helping the Japanese protein crystallographers with some beamtime. Thank you very much for reading this message thus far and,
faithfully,
Soichi
Soichi Wakatsuki, Ph.D.
Professor and Director of Photon Factory and Structural Biology Research Center
Associate Director, Institute of Materials Structure Science, KEK
***
The most currently information about KEK can be found here.
Tidbits:
Work began on hemoglobin in 1937, which led to a low resolution in 1957 and completion in 1959. Perutz mentions struggling with the phase problem until 1953, which is 16 years after beginning the project. He ended up using the heavy atom method to solve the structure.
Max Perutz, “In retrospect, you know it looks… like this marvelous persistence carrying on like that but… I carried on out of desperation.”
The following is an unedited letter by Dr. Soichi Wakatsuki who is the director of Japan’s Photon Factory, a national synchrotron radiation facility. The letter is a perspective on the magnitude 8.9 earthquake that struck Japan on March 11th. The facility is located about 40 miles north of Tokyo, which is toward to epicenter of the earthquake (depicted as a red square).
