Leginon

As nitrogen refill is needed once every two hours, most users here just live with it. We do not yet have a automated filler that is integrated with Leginon. You may pause Leginon maually when you fill and then continue Leginon after a few minute.

"anchi" wrote: As nitrogen refill is needed once every two hours, most users here just live with it. We do not yet have a automated filler that is integrated with Leginon. You may pause Leginon maually when you fill and then continue Leginon after a few minute.

The recent paper on contamination build up (A Cheng et al 2006 JSB 154, 303-311) briefly describes automated liquid nitrogen top up of the cryo holder dewar n the materials and methods. Has the automated filler been integrated with Leginon yet? Also, on longer Leginon runs it is necessary to top up the cold trap dewar as well. The paper says that the cold trap dewar was modified to only require filling every 8 hours. What sort of modifications were carried out? An UIUC technical report ("00-002: An automated system for maintaining liquid nitrogen levels in the Gatan cryostage" SJ Robinson et al) describes an approach to automated top up of LN2. It mentions that the cold trap dewar was larger than usual with a different attachment/ platform to support the larger dewar (and needed to be topped up every 12 hours). I'm not sure if using a narrower neck opening on the cold trap dewar might help and also when using a larger cold trap dewar if the neck opening must at least be kept constant in size (i.e. no bigger than the original cold trap dewar)? We are interested in automated top up of LN2 in Leeds partly because student interns are less available for this task. We have looked into using the Norhof system for top up of the cryo holder; but top up/ using a large cold trap dewar and synchronisation of cryo holder top up with Leginon still are problems that have to be solved,

William

Most people who are using the Norhof system here are only using it for the cold trap dewar, not the cryo holder. It is commonly used to keep the cold trap going while Leginon acquires data all night from a non-cryo grid.

For Anchi's contamination study, the Norhof was rigged up to fill the cryo holder, but this was not optimized in a way that would be necessary for high resolution data. That was ok because she was only taking intensity measurements, not high resolution data. If high resolution data is required, we would have to properly integrate the Norhof with Leginon so that acquisition does not take place during the fill cycle. Also, a special drift check would have to be done after the fill is complete to deal with the thermal changes. And maybe the most difficult problem would be to fill it up in a way that does not cause a long term bubbling and vibration.

The aparatus described in the tech report: http://www.itg.uiuc.edu/publications/techreports/00-002/system.htm

was more primitive than the Norhof system. We called it "the bomb" because it was gravity fed and you had to suspend it above the level of the cryo holder. It was a little scary hanging the big dewar filled with LN2 from some wires hanging from the ceiling. The Norhoff system has a much better and safer design (any comment on this, Anchi?)

The cold trap system was made to last longer by using a larger dewar (maybe 3 times bigger). This larger dewar is about the same height, but a larger diameter, so a new platform was built to support it. We also had to build a new foam cover to fit this larger diameter opening. It may last longer if it had a narrower opening.

Jim

Since this post there is a paper that came out in JSB in 2010 where they used the Norhof pump to refill a gatan side entry stage along with Leginon. We have a CT3500 which has a smaller opening than the 626. What is the current feeling about this set up and are there any modifications that should be made? Does it work well and is the Leginon node available and widely used? Thanks
Bob

We have not used the pausing server William Nicolson wrote at NRAMM. His server/client pair for pausing Leginon in preparation of Norhof pump was not deposited to our svn. Only the lacey carbon hole finder was deposited into Leginon. You will have to get that application from him. We had used similar Norhof pump filling nitrogen without pausing Leginon in refilling a few years ago. We did have vibration issue. William's solution would certainly resolve that problem. The other unsolved issue was that, since the dewar need to stay uncapped, the fill tube dripped water into it when the condensation melted between fill. Jim made an reverse funnel over the dewar opening, and it helped some. It was tried out for ice contamination study where high resolution was not required. We have not use it since.

Anchi