900 News

Test Library Now Available!

2006-06-28T12:37:00.000-07:00

Now that the testing phase of the spectrometer is complete we would like to make our findings available to our users and to the NMR community. It has taken a lot of effort to bring the system up to the high level of performance that it is at now and we feel that there is no point in keeping the fruits of this labor under wraps. In posting this information we have made efforts to ensure that each data set is representative of the average performance of the system, and that the results are reproducible. It is our hope that these parameter sets will be useful not only to our users, but to anyone who is evaluating a new or existing system. In order to keep track of the demand for this information we ask that users register prior to accessing the library.

Check it out at http://biomol.uchsc.edu/rm900/testlib.html

Open for Business

2006-05-30T13:31:00.000-07:00

We are pleased to announce the opening of the Rocky Mountain Regional 900 MHz facility to users! Proposals may still be submitted if you would like to request time on the system. We are requiring that users visit the facility to set up their first experiments, and we will set up access for future experiments to be conducted remotely if so desired. For the first few months of operation we are prepared to offer the spectrometer time for this initial visit free of charge. We are looking forward to meeting all of you and hearing about any specific needs you may have. Your comments will help to make our facility better for everyone.

ENC Meeting

2006-04-19T11:23:00.000-07:00

I will be attending the ENC meeting at Asilomar next week. If anyone would like to meet to discuss anything about the facility, or just to get to know me and put a face with a name, I'll be available throughout the conference. Send me an email, or give me a call and we can work out a meeting place and time. I'll be posting a note at the message board with my email and cell number when I arrive. Hope to meet some of you there!

Almost there!

2006-03-27T08:45:00.000-08:00

We are just a few weeks away from being open for business. Most of our testing has concluded and Varian is finishing up with the last of their remaining issues. So now is the time to finish up your proposals and get them to us for approval. If you require some notice to prepare samples and/or travel arrangements, make a note on your application and we will contact you for scheduling. Otherwise we will start scheduling users from day 1.

There have also been some inquiries during our testing phase that I would like to share with everyone:

Q: What sequences do you have available for immediate use?

A: We have the BioPack suite of sequences installed and tested. We have optimized parameter sets for these experiments available as a starting point for initial work on the 900. We also have tested sequences from Lewis Kay's library, but many of these have been optimized for large deuterated molecules and do not work as well with our ubiquitin test sample. These sequences will be available for users by request. All other "in-house" sequences must be pre-screened before being used on the 900.

Q: What is your policy on remote operation?

A: Currently we are not allowing remote operation. Initially we would like all users to visit the facility and go through our orientation program before using the spectrometer. After this initial visit we will consider remote operation applications.

Q: When will the cold probe become available?

A: We have a salt-tolerant cold probe on order from Varian. The current delivery target for the probe is in May. We hope to have the probe installed and tested by the end of the summer, but it is too far in advance to make any specific estimates.

Q: What is the cost for spectrometer time?

A: We are still covered by the NIH grant for the system, so initial costs will reflect our facility expenses only. We have not yet worked out an exact number, but we expect to charge a similar fee as the current cost for the 800 facility in Boulder (approximately $4 an hour).

Q: How much spectrometer time can I request?

A: We are anticipating offering substantial blocks of time to our users so that multiple or long experiments can be run. The actual amount of time will depend on demand, but it is possible that time requests up to 2 weeks long may be accommodated.

I hope this addresses some of your questions, if you have any other inquiries please do not hesitate to ask me and I will do my best to address them. We are looking forward to hearing from you.

Accepting Proposals

2006-01-06T14:22:00.000-08:00

Testing of the spectrometer is proceeding smoothly and we anticipate being able to open the facility up to users in the coming months. As the facility was funded through a consortium grant, we have established a committee of users that will be in charge of approving projects for the system. All interested users are encouraged to submit an application outlining the proposed project. These proposals will be reviewed by the committee and time will be awarded based on merit and applicability for 900 MHz. Users from within the consortium will be given priority, but proposals from other publicly funded institutions will also be considered.

We request that potential users be available to travel to the facility to collect data, as we will be providing on-site training. Once users have visited the facility and undergone the training program we will consider requests for remote operation of the spectrometer.

We are looking forward to seeing the exciting new projects that you will bring to the facility!

Probe comparisons

2005-11-09T12:23:00.000-08:00

Just a quick update. We've been collecting a lot of data over the past couple of weeks, checking for anything that might be out of place. Varian has sent another probe out to us with an engineer to run some comparisons of the performance of each probe. There are some improvements that we want to see before we move ahead with testing. This will probably slow us down a little, but is to be expected in the installation of such a high-end piece of equipment.

Facility Testing

2005-10-27T10:35:00.000-07:00

Facility testing has been going on this week as we establish a baseline for the performance of the system in years to come. Our overnight tests of the drift rate are now coming out at less than 3 proton Hz per hour! All of the multi-dimensional protein data that we collected on Ubiquitin is looking great and we can't wait to see some results from a more challenging sample. We have also been able to improve remote access through the campus network so that it will be easier for users to log-in and get their data from afar. The coming months should prove to be very exciting!

Next Phase

2005-10-21T08:30:00.000-07:00

Well this week we have been finishing all of the tests with Varian. Monday the spectrometer will be handed over to us to begin our facility tests. We have established a stringent series of experiments that will give us a clear idea of how the spectrometer is functioning so that if there ever are any problems down the line we can easily run the comparisons. We still have a few issues that have not yet been settled with Varian so negotiations are ongoing, but we can continue progress while that goes on. As we get closer to opening up to users we are looking out for ways to make the facility even better. As always we welcome questions and comments!

Return of the probe

2005-10-11T10:25:00.000-07:00

The probe is back now and we will be testing it thoroughly over the next few days. They could find nothing wrong with it back in Palo Alto, so we'll see if anything has been fixed at all. We've used the lull to complete a few updates to the facility, in particular installing the UPS to power the console. In a test we performed last week with the console idle the UPS supported the power usage for 3 hours without line power. This is well in excess of what should be required for the system, as all of the power is backed up by the campus emergency generator. We had an actual test of the power back-ups this weekend as we had a brief power outage Sunday morning. Apart from calling me in to check on things the system weathered the outage without any problem.

Some bad news

2005-10-05T12:57:00.000-07:00

During one of the installations tests we encountered a slight problem with the probe. We are sending it back to be checked-up and should only be down for a couple of days. We'd rather have this happen now than further down the line. Other than that the tests are still progressing well, we've only uncovered a few minor concerns so far.

3D Data!

2005-09-27T13:54:00.000-07:00

Here's a small section of a 3D CBCA(CO)NH strip plot of Ubiquitin. This spectrum was acquired in 16 hours as part of the testing and installation of the Varian NMR system.

Lineshape stability

2005-09-20T11:57:00.000-07:00

We've accumulated some drift data over the past few weeks and all is looking very good. The magnet drift is down at 4.5 Hz per hour, and the lineshape drift meets spec easily over a 12 hour period. This spec was due to be met 6 months after magnet energization so we are very happy to see it come in early.

Weekly Update

2005-09-16T12:18:00.000-07:00

Well Varian has been working hard all week to achieve the sensitivity spec for the system, but so far has been unable to meet the sucrose test requirements. They are doing a lot of troubleshooting though and seem to be progressing well. We have been checking on some vibrations as well this week and are tweaking the facility to get us the best possible results. This installation has been a good test of our remote operation capabilities, so the process of running the spectrometer from remote sites is almost completely ironed out. We feel that this is incredibly important for our users, as not having to travel to Denver to operate the system will substantially decrease the cost of using this facility.

Solaris 10 and VNMRJ

2005-09-07T08:47:00.000-07:00

Remote testing has begun, although we ran into a snag yesterday with loading the shims for an experiment. Apparently VNMRJ does not play well with Solaris 10. So we will be downgrading the system today to Solaris 9 in the hopes that some of the inconveniences we've been experiencing will be alleviated. Apart from that things are still progressing here on schedule.

On-site installation

2005-08-29T15:15:00.000-07:00

The on-site installation is almost complete. The console is set up and all tests are going smoothly. However, there are still many tests to be performed to gauge the quality of the system, these will be performed either remotely by Varian personnel, or by the facility manager. Some of these tests are required after the magnet has stabilized for three months, so if everything passes, the final installation and acceptance may occur in November. This is an approximate timeline, of course, but as we progress further, we will be able to be more specific.

Drift coming down

2005-08-24T15:51:00.000-07:00

The magnet appears to be settling very well. The last of the cryoshims were put in last Thursday, and by Wednesday morning the drift was down to less than 6 Hz/hr. In addition it seems that there is very little drift in the shims, leading to a very stable lineshape. Tests are ongoing, but so far everything seems to point toward a great system. We are looking forward to opening the schedule up to users in the coming months. Keep checking back for updates and information on submitting proposals.

No strings attached!

2005-08-18T12:18:00.000-07:00

The superconducting shim coils have all been set to their final values now according to the mapping data. So the leads have come out and the magnet is on its own for the first time. From here, the magnet will have to be mapped again, and the initial values for the room-temperature shim coils established. Then work on the calibration and acceptance tests can begin. We will be receiving the room-temperature triple resonance, triple axis gradient probe tomorrow. If you are interested in what tests we will be running before accepting the magnet/spectrometer, don't hesitate to contact us.

By the way, the star of this photo is Oxford's own Chris Morris, who has been with the spectrometer from its initial cool-down to full-field. Credit for the assembly of this magnificent instrument goes to Will Mander, who can be seen in several of the installation pics.

First Data

2005-08-17T15:39:00.000-07:00

Well, as the mapping has begun I thought it appropriate to snap a quick pic of the very first spectrum run at 900 MHz. An exciting moment indeed!

Cryoshims

2005-08-12T09:54:00.000-07:00

Just an end of week update! The cryoshims are all set to within 0.5 A of their factory settings. When Varian arrives next week, the field will be mapped and the shims will be dialed into their final values. Once that is done, the leads will be removed and that will mark the end of Oxford's involvement (as long as nothing is out of spec). The fridge will also have to be adjusted to minimize helium loss.

We have been hard at work getting the Sun workstation ready to run the console. Since we are not running experiments with it yet, now is the time to make sure it is set up properly for future use. In particular, remote operation is a key requirement. We have installed a VNC server on the machine which will allow users to run the computer from their desktops with very little latency across the network. Unfortunately it appears that vnmrj-2.1A does not play well with VNC, so we will have to appeal to Varian to get it working. We also will need to discuss with our IT department how best to forward outside traffic through the campus firewall to the spectrometer computer. We think remote operation will be the best option for our users in the future, so we are working hard to accomplish these goals.

As always, we are happy to hear from our potential users, so don't hesitate to contact any of us with your comments and questions.

[Update 08/12/05 2:39PM]
We have fixed the problem with vnmrj and VNC connections!

Update

2005-08-09T15:43:00.000-07:00

Chris has arrived and has begun putting in the cryoshims. This magent appears to be rather well behaved as none of the cryoshims were very large in the factory. This bodes well for drift spec. Our eventual drift came out at about 4.5 proton Hz/hr after the 10 days of settling. This will of course change slightly as the shims settle in, but is a good starting point. Next week (the 15th) the Varian engineer will arrive to set up the console and map the field. Stay tuned!

Field Drift

2005-08-01T17:31:00.000-07:00

The magnet has already settled well, over the weekend the drift rate was approximately 3 Hz/hour. This is already well under spec, so it looks quite promising. Hopefully everything else will come in just as well.

We have also added a user forum to the website. This is designed for users of the facility to interact with the managers, and with each other. Asking questions and sharing ideas is welcome here, we hope it will be beneficial to all!

What now?

2005-07-29T14:58:00.000-07:00

Well now that the 900 is persistent at full field, what is next? The console (the Varian NMR System) has been delivered and is ready to be set up, but the magnet must first be allowed to stabilize for 10 days. This will allow the drift to settle in. Once the magnet has settled, the cryoshims will have to be run in (taking about 4 days), and then the magnet will start going through its final installation and testing. We have a long list of tests that must be run before the magnet/spectrometer will be accepted. But so far things are on track and we are hoping to be up and running soon. In the meantime, we will be working on improving this site. All potential users should feel free to make comments and suggestions for the facility, and participate in the online community that we will be setting up soon. We look forward to hearing from you.

900 at Field

2005-07-29T09:12:00.000-07:00

The 900 went to field yesterday Thursday at about 11.30 am, and has been stable now for almost 24 hours.

Overnight drift looks promising, a little under 10 Hz an hour.

Update on 900

2005-07-27T15:44:00.000-07:00

Well we reached 111 amps, its an 880 MHz. Geoff still has not seen the big Q. Lets keep our fingers crossed that it will be a long while before he does. We are leaving the magnet overnight to settle. Tomorrow will be 900 or bust!

Status of 900 Energization

2005-07-26T15:10:00.000-07:00

Today we reached 105 Amps, that makes it an 832 MHz system.
It will be parked overnight and then tomorrow we go to 111 amps.