ASI policies at Beamline 8.3.1

Crystal Submission and Data Collection

All protein crystals shipped from Alberta to the ALS for data collection at beamline 8.3.1 must be entered into the ASI crystal database. Crystals for which there is no information in the ASI web database will not be shipped.
The labels of the vials and canes that contain the crystals must correspond to the labels in the web database. The canes have to be labeled with the user's ID and up to two additional letters (e.g. emb1-embZZ). The vials should be labeled similarly with the user ID, cane number, plus an additional number (e.g. embZZ1). This crystal ID will be used as a default prefix for the X-ray diffraction data.
No other labels or markings on the vials please, except pin size (typically 18) or loop size (e.g. 150µm), if applicable. No other names and prefixes for the crystals please.
Please use only the bottom three slots of a cane. They are referred to as bottom, middle, and top in the database. The position of the vial in the cane must correspond to the entry in the web database.
Please input as much information as possible about the crystal in the database and if at all possible screen, index and strategize the crystal at home. Also please prioritize your crystals and indicate for similar crystals which ones are better.
If the crystal is very difficult to spot in the loop please provide a snap shot, screen capture or sketch of the position of the crystal in the loop. If applicable indicate the best position for the X-ray beam on the crystal.
The X-ray diffraction data will be transferred to a local disk at the U of A after data collection. The location of the data (path) can be found in the run information on the web database entry for the crystal.
Users should back up their raw X-ray diffraction data on a hard medium soon after data collection. ASI and the beamline attempt to keep complete records and DVD backups of all data collected by Alberta on beamline 8.3.1. Because all media (CDs, DVDs, hard disks) can fail users should not rely on these backups and make sure they have their own.
Data collection priorities will be decided upon just prior to the beam time based on the user input in the web database and the most efficient use of beam time.

MAD Data Collection Instructions and Strategy

The following information and guidelines have been prepared by Ernst Bergmann regarding MAD data collection on beamline trips to BL8.3.1, and are expected to be applied on a crystal by crystal basis. They are also generally applicable to any MAD data collection.

When collecting MAD data one tries to collect data sets that maximize the anomalous and dispersive difference within the data collected from a single crystal. One also must try to record the intensities of Friedel mates in the shortest possible time span.
At a modern third-generation synchrotron beamline (such as BL8.3.1) the damage to the crystal is significant and the resulting decay of the intensities will have a devastating effect on the anomalous and dispersive differences that one relies on for phasing. As a rule of thumb, three to five minutes of total accumulated exposure time is all most protein crystal can handle. Keep in mind that the small differences in intensities that are essential for MAD phasing are disappearing fast and before you notice significant decay from looking at your images.
Damage to the crystal is worse at longer wavelengths.
Several studies have shown that collecting highly redundant data is the most critical component of collecting good MAD data. The data need not be complete; 85% to 90% completeness is often enough. Do not attempt to collect high-resolution data unless you can do so with very short exposure times. Getting good phases from a data set with no decay to a resolution that is sufficient for phasing is the goal.
Do a strategy once you have indexed the crystal and decide on a reasonable minimum sweep that will give you 90% or better, also of Friedel mates. Pay attention to the maximum possible oscillation range and bear in mind that that depends on a reasonable estimate of mosaicity. Mosaicity can be difficult to estimate and is, usually, different along the different reciprocal space axises. If in doubt use a conservative estimate of the oscillation range.
Choose a remote wavelength so that it is far enough away from the absorption edge to maximize the difference in f’and f”, but close enough so that the same reflections are observed on the same image. If you move more than 1000eV away from the edge the diffraction pattern will be quite different. (200-500eV are usually a good estimate).
Ideal MAD data sets are collected as three wavelengths (peak, inflection and remote) with inverse beam and in small (1° to 10°) wedges. For many crystals, especially those with low symmetry, that is not even possible with very short exposure times.
If only two wavelengths are possible and the fluorescence spectrum gives a clear indication of the peak wavelength it is best to collect a highly redundant two wavelengths data set with a peak and remote wavelength.
In the case of L-edges and derivatives with low occupancy sites the peak wavelength could be obscured by a XANES spectrum or noise. In that case it is safer to collect a two wavelength data set with inflection and remote energies.
If it is only possible to collect a single wavelength in the time available it is best to collect a redundant, peak, SAD data set first.
It is often a good idea to set up two complete data collections with a short and long exposure. In the case of MAD data collection the short exposures should be collected first and yield the required phases. The longer exposures may yield additional phases but more likely higher resolution data for refinement. Similar data collection schemes are even useful for monochromatic data collection if long exposures lead to overloads in the low resolution data. This can be a problem with CCD detectors at modern beamlines. The data sets can then be integrated separately and subsequently scaled together.

(Examples of very good and successful data sets recently collected at BL8.3.1 are "bkb162" from 02/19/04, "bkb141" from 02/20/04 and "bkb301" from 02/20/04).

Data Storage and Transfer

All data collected at Beamline 8.3.1 under the ASI access program are transferred from the beamline server to a local terabyte raid storage facility in the ASI offices. The data are then made accessible for dowloading by researchers from individual accounts. In order to download, you will need to know the following information:

Server and Directory Information

Server: bollux.asi.ualberta.com

Usernames and passwords will be provided on a per-research-lab basis, please contact for more information.

Server Access

Access to the server is limited to secure ftp connections. Following are some instructions for downloading your data depending on your operating system.

1. Unix (commandline):

scp -r nggroup@bollux.asi.ualberta.com:data/apr20/JHO01

2. Windows:

a nice and free sftp gui can be found at
http://www.ssh.com/support/downloads/secureshellwks/non-commercial.html

3. OSX:

a nice sftp gui is fugu
http://rsug.itd.umich.edu/software/fugu/
or you can use the command line.

Data Backups

We highly recommend that you backup your data on external media (e.g. DVD) after retrieval from our raid server. Both the ASI and the staff at beamline 8.3.1 try to maintain a complete record of all data on external media; however, since all media is subject to failure, this should not be relied upon exclusively.

Data storage on the raid server is subject to space limitations. Our current intention is to maintain the data for a minimum of three months and a maximum of one year. We will send out notices before deleting data sets to ensure a minimum inconveniece to users.

Data and Computing Policies on the Beamline Computers (from James Holton)

Here are some tips and pointers for 8.3.1 Beam Team users in 2004. Some of these "tips" are just about basic computer courtesy. I hope that everyone can agree that the beamline's main purpose is to collect data. Remote processing comes second. I would like for people to be able to login and process data here after their collection is done, but you must be careful not to mess things up for people who are trying to collect!

Unfortunately, there have been some recent "incidents" of legitimate users logging in remotely and (I assume unintentionally) breaking various things while other people were trying to collect data! About 30% of my time this week was spent cleaning up after a few careless and sloppy people, and this is not fair to the people who are on-site and need my help. So...

Some tips:

When processing remotely, use /local on crush13

Each "crush" node has a fast, local disk called /local that anyone can put files in. It is much faster than using /home (over the network) and will not interfere with someone who is collecting, and needs to process quickly. Crush13 is set up to share process space with other "crush" computers, so even if it looks "busy" it's not. So, if you are processing remotely, just do this:

cd /data/mcfuser/
tar cf - your/stuff | rsh crush13 "cd /local/mcfuser ; tar xvf -"
rsh crush13
cd /local/mcfuser/your/stuff
Elves .

Transfer files home from the file server

The computer you log into when you connect to "bl831.als.lbl.gov" (or "server" from the graphics terminals) is the computer with the local /data disk. So this is the best place to launch file transfers. Launching a file transfer from a graphics terminal or a "crush" node requires the data to go back-and-forth three times over the network, and just slows things down

Do not run jobs on the file server

The computer you log into when you connect to "bl831.als.lbl.gov" (or "server" from the graphics terminals) is also running all the data collection control system programs, and it is also the slowest CPU at the beamline. Running a processing job here may cause the detector to hang in the middle of collection. If I catch anyone doing this, I will kill your job (and, perhaps, you) without hesitation. ;)

/data is for data

The /data disk is optimized for high-speed access to large files. Putting your processing files in here will significantly slow down data collection because of the "high-transaction" NFS load that processing puts on a disk, and because the millions (yes, there are millions) of tiny processing files will cause a disk with a large block size to rapidly fill up. /data actually "filled up" at 50% once. I am now in the habit of regularly moving peoples processing files from /data to /home so that /data does not get fragmented.

/home is for processing

The /home disk has been optimized for processing. Small block size, and a located in a different computer from /data gives a significant (30-50%) improvement in data processing speed and prevents processing from slowing down or crashing data collection.

/data2 is for emergencies

There have been times when I told people to collect here, but that was because /data was full. We are pretty good about keeping up with the backups now, so this shouldn't happen anymore. Use /data2 only if /data fills up in the middle of the night.

Only /data is monitored by the DVD robot

/home and /data2 are NOT! Every 5 minutes, the DVD robot checks for any new images on /data. Once you have enough to merit a DVD, or when the name of the user changes, the robot will write a DVD. Unfortunately, the robot cannot tell where a new file came from. It expects that all new files are newly-collected data. So, if you are a Credle, and you copy some old data back onto the beamline while somebody else is collecting, the archiver will start rapidly switching between "users" and make a big pile of DVDs with one image file on each. (this could get expensive)

Use the "-p" flag in cp and scp

This flag will make sure the date on your files does not change when you copy it. Not only is this nice to the archiving system, but it will help you in the long run figuring out which files are what.

Do not "touch" your files to keep them around

Trying to hide your files from the "reaper" that cleans up the /data disk periodically by making them look like recently-collected data is dishonest and also doesn't work. The "reaper" program is now smart enough to recognize files that are out of place and will delete them immediately (without backing them up first!).

Feel free to change your filenames, but...

Changing your file names or moving data into new directories is something that you do want to be able to do while you are collecting. This is the only reason why I don't make the /data disk read-only like all the other ALS beamlines. However, you do run the risk of confusing the archiver, and your data may end up with it's old name on the DVDs (depending on when the DVD is triggered).

Also, programs like "download" that follow the data collection log won't notice moved files. Basically, if you rename stuff, check that it transferred correctly.

Do not put multiple copies of your data on disk

If anyone can come up with a good reason why why this is anything but a complete waste of space, I'd like to hear it.

Do not put files in generic directories

Please put your files under a directory that contains your name. This makes it easy for the archiver (and me) to find your data in case you need it restored some day.

Do not delete other people's data

This hasn't happened yet, and I hope this "rule" doesn't suprise anyone.

Do not delete your own data

This is my job. My big research project at the beamline is studying how to make beamlines more efficient. I need a complete record of the data quality collected at 8.3.1 to make this happen. (this includes snapshots!)

The beamline is not an overflow disk

I know that the home labs can be strapped for space sometimes, but please don't try to use the beamline data-collection disk for long-term storage. It's unfair to people who have new data and really do need access to it. Besides, I've got everything on DVD here anyway, and I'd be more than happy to restore some old data that you might need, or to make a DVD of it for you.

I hope that this will help people work more efficiently at the beamline in the future. And when you work more efficiently, we all have more time to play.

-James

Travel Claims

The Alberta Synchrotron Institute Protein Crystallography Project pays for researchers to fly to Berkeley (and some other locations) to conduct research and, in some cases, to attend training courses. As we are operate under the jurisdiction of the VP Research office at the University of Alberta, travel claims are processed through University of Alberta Financial Services.

There are specific policies regarding the receipts and information necessary for travel claims, some of the most important are listed here:

Per diems. Recently the VP Research office has set a policy with us regarding the claiming of per diems, which differs from our previous policies. From now on, if you are leaving before noon (departing from the University) you can claim a full day's per diem ($45US), otherwise we are only claiming supper ($25US). Alternatively, you can submit receipts for food expenses for the first day. Return flights are not usually an issue, since we usually arrive late in the day. If it transpires that you need to collect for breakfast and/or lunch, each meal is valued at $10US.
Flight receipts and boarding passes. We need *at least* two documents for the flights that are taken. The first is a detailed flight receipt, showing both the booking (itinerary) and the fees for the flight. The second requirement is all of your boarding passes. Financial services require both of these to calculate the GST they can recover and also to confirm that you actually took the flight.
American funds. If you are using an American booking service (i.e. AlaskaAir.com) for your flight, or paying for specific items using US dollars (i.e. transit, hotel) then you can calculate the conversions two ways: either by providing a credit card statement with the charges indicated on it (in addition to providing the detailed receipt) or by using the OANDA converter or credit card converter which you can find linked from inside the travel claim forms. Credit card charges are higher than the straight conversion, make sure you add the 2% credit card charge on these transactions.
Appendix for travel claims. The ASI travel claims are trust funded (there is a check box on the travel forms) so you need to complete the supplemental travel information form (intriguingly entitled "Travel Claim Attestation Form Research/Trust").
GST. Canadian claimed funds have an associated GST amount. For items in the Tax Added (TA) section of the travel claim, this number is calculated automatically (eg. for cab fare). For other items (eg. Canadian plane fares), you need to explicitly indicate this amount as found on your detailed receipts. These numbers are required because the University is reimbursed for some GST expenses.

You can find all the relevant travel forms on the U of A forms cabinet page

We try to process your travel claims as quickly as possible, but we are only the first step of three; we pass your claim to the VP Research office and then on to Financial Services. If your claim does not have all the documentation, it can take an extra week or two for your claim to be reimbursed. If you have any questions or concerns, do not hesitate to contact either Jonathan in the PX group or Paula in the office.

Specific Policies for Data Collection at 8.3.1