Beamline 8.3.1 - MSG User Guide

To open the hutch:

Press the photons off button to stop the beam.

Press the Door open button, then hold the door open button down while opening the door.  Good, safe, yet simple.

Want to know when your data set will be done?  type "eta.com" and the script will look at the current runs goals, the time stamps on frames being produced and give you estimates of when it will finish updated every frame or so.

The spot shape on detector options on BLU-ICE hutch tab don't currently work.  Instead, type "divergence.com" to see current values (usually 2.0 0.5).  Type "divergence.com 0.5 0.5" to get smaller slits for example.

Two-theta works.  Enter the value you want in the two-theta window on the BLU-ICE hutch tab.  As usual, press "START" to apply the changes you've entered and actually move the detector to that two theta value.  Note two things: 20degrees is a lot as you'll see if you ever lift it 20, especially if you are far back.  Be very careful using 2theta when you are close in.  It should be OK, but watch out for detector/apparatus potential collisions.  And third of two, note that the resolution predictor won't work at the two theta angle.  You can estimate the beam center position (tan(2theta)*detector distance) and subtract this off of the y value in adxv "settings" to get an approximation of the beam center.  If you have close spots an even better idea or in addition, is to take a direct beam.

Direct beam: Put in all the foils (Se,Cu,Al), set exposure time to 0.1 sec, use an energy effectively absorbed by the foils (1.1 A (~11200) should be OK)

Every few hours you may want to check and tune up the beam alignment.  You can do this by typing tuneup.com in a window or use the "optimize beam" button in the hutch tab of BLU-ICE.  Either one will move your crystal safely out of the way while it does its thing, generate a few graphs, and bring your crystal back when it's done.  Note that when it reports beam intensity as a percentage of max, the max possible may not take into account slit adjustments or other sundry things you may have on.

Given the camera view is down the axis of the beam...i.e. you see what the photons see, then with phi=0 you can use the Y-axis to move the crystal in and out of the focus plane. 

As of March, 2002 there is a swing out shelf in the hutch that swings under the crystal or stows under the platform.  It has a tacky (literally) surface which makes it kind of exciting (read treacherous) to get very full wide LN2 dewars off of it.  Turns out there's a switch that senses the tray position, so you can't drive the motors while the shelf is out.  (i.e. Detector could collide with it, collimator set up could collide with it...)  So be sure the shelf is fully returned to its stowed position and tray tables and seat backs are in their upright position before you attempt take-off.

If the phone rings in the middle of your night shift, and you groggily answer it, "line 8.3.1, hello?" and a voice shouts back "8.3.1 WHAT THE HELL ARE YOU DOING WITH THE SHUTTERS?!?!", it's probably just Luke helping keep you awake.  I found out that this works quite well.

I don't know if the following still applies.  Probably basically the same, but easier to realign afterwards with James' new scripts.  Haven't done it myself yet.
020331

Ok, you want to change the pinhole. Are you sure?  The 30 micron one gives very clean spots at the cost of some intensity or whatever the proper term is.  But after you do it you're going to wonder if you really should have done that.  If you do change it you are most likely going to have to align the beam (see following section).

Still want to change it?  Allrightee then...

Please be careful as space is very tight on this setup so there is little room for manoeuvering.

You will notice that over the back of the pinhole shaft is a copper "strap" held in place by a set screw. Unscrew the set screw, freeing the copper strap to rotate away (towards the beam) and then pivot up, so you can now freely lift the pinhole out of the way.  Note how the pinhole is sitting in the trough so you can put the new one in the same way. Its metal base disk is flush against the mount, etc. unless I left it in wrong (just kidding).  So find the new one, lower it carefully in to place, resecure the copper strap under the set screw and it's done.

If you  are worried about the alignment, James wrote a script called getaxis.com.  This compares images to find the true center and provides output that is meant to be fed into stage.com, which moves the stage up and down.   So you then type stage.com plus the info from findaxis.com.  Now you want to define that point as the center of rotation and the default zero value for where the stage returns to when it is unparked.  So you enter "stage.com zero".

All this below may be somewhat obsolete now:
Ok, you arrived at the beam and the little white centering box is nowhere near the middle, someone has put in the pinhole/collimator you don't want to use, and when you do inverse beam only one wedge is showing any spots...Chances are the beam isn't where you think it is because you changed the pinhole or something, or someone bumped it or whatever.  If your crystal is on the beam you may need to take it off unless the X-rays visibly affect your cryoprotectant in which case you might be able to use that to visualize the beam position.

This is more simple than it sounds particularly after you've done it, but after talking some people through it over the phone, James will probably write a script to do some parts of this for you, so be prepared for updates/changes.

If you can't see the beam hitting your cryoprotectant, you need to remove your crystal and find the 'YAG & center thread' thing-a-majig which was last seen in the "alignment jigs" box.  It is on a magnetic capped crystal pin in a vial.  There are two of them in there.  You want the one with the triangular piece of yellowish plastic looking stuff (about 3 mm across its broad edge) with a small thread sticking off.  Put phi at 0 degrees, and have the side the thread is glued to facing the beam.

Center the thread on the rotation axis using a point (on the thread) about 1 mm off the end of the yellow plastic stuff.  Now move the Z-axis 1500 units (one of the boxes under the "setup" tab in the centering window) and you should be on the YAG.  If you have phi=0 the Y axis then corresponds to the axis of focus, so move Y to focus on the surface of the plastic.  If you picked a spot on the thread pretty near the same plane as the surface you should only have to move ~70 ticks or so.

Now open the shutter and observe the beam position.  You can control the white box on the TV monitor using the 4 knobs that extend horizontally from the base at the lower left.  Set the box to bound the beam circle.

You should also move the green cross-hairs of the control computer's centering window to mark the beam center location.  You do this by right clicking on the position where you wish the cross-hairs to be and answering "yes" to the query about whether you wish to move/update them.

Good...you're almost there.  Now of course, we want to move the center of rotation to coincide where we have discovered the beam to be, marked as it is by the green crosshairs.  So go back to the thread somewhere (reverse the Y and Z movements you did above if you like) and center it on its own center of rotation.  Note for those of you doing this in the middle of your hazy brained night shift...if you moved the green cross hairs this is no longer the center of rotation so you can't center the thread there.  So put some recognizable feature of the thread on the green cross hairs, now rotate 180 degrees and then middle-click on this feature which will move it half-way back, thus centering it.  Repeat that for the orthoganol axis so it is fully centered, or centred if you're from across the puddle.

Now we need to move that centered thread to be on the green cross-hairs, so move the vertical collimator up or down by small increments (~100 units) until these line up perfectly.  (Side note:  if you are going to the trouble of doing all this, I implore you to please do a good job.  It will help your experiments, it will help the next person's experiments and we won't all be wondering what the hell happened to the beam in the shifts before us, who bumped what, and just where is the beam actually at. And if we're all doing a good job when we have to do this, one day it will come back around and when you arrive at the beam everything will be finely tuned, ready to go, and trouble free.  Pay it forward, man.  What a tearjerker that film was.)  OK, so where was I...oh yeah.  You've now got the actual center of rotation lined up with the green cross-hairs that mark the actual beam position.

All we need to do now is to set this position of the vertical collimator to be zero so it finds it every time.  On the "Centering" window, under the "Setup" tab, there is a list of programs down the left column. Click on "Direct/Vertical Collimator".  Now is the time to open up your secret decoder ring that you got in the Captain Crunch cereal box that was distributed in the goody bag at last weeks "Meetings of the Sekret Society of Stinkrotron Socialites."  Oh...did you forget to attend. Well I'll give you the code anyway...in the "Send Command" box type these characters and then press return:   #4hmz

Alllllright!!!!  Mission accomplished.  Congratulations. You should be ready to go.  Park the hutch stuff, take off the alignment jig, put your crystal back on or whatever you're going to shoot next.  You should probably run the tuneup.com script to optimize the beam, and you're G2G. Gee, I hope I remembered this stuff correctly.  And if this doesn't work or you break something trying this, well I never told you to change the pinhole, pinhead.  Errrr, I mean good luck!

Use the scan tab on BLU-ICE, select the appropriate element you want to scan for, press scan.  Will do plot, analyze (I think with CHOOCH) and give you the inflection and edge.  Fluor detector is automatically positioned.

James has a nice Kapton tape mount that you can press your greased cover slip onto, thus shooting the drop with absolutely minimal manipulations to the crystal. It's very nice and complemented by the fact that the camera looks down the direction of the beam, so what you see is what you get.  If you are using this, which should be supervised by James or someone who's done it before the first couple times, you CANNOT and MUST NOT rotate around phi when the collimator set up is up and in position as it WILL bang into the collimator and stuff.  You can rotate phi and get the crystal in focus with the collimator set up down and out of the way, make sure you are back at phi=0 (and the cover slip is therefore normal to the vector of the beam by this definition) before bringing up the collimator stage.  And then remember, once again...do not rotate around phi and make sure all snap shots are set to take pictures at phi=0, or if you really must, +/- ~10 degress.  Really, I wouldn't go trying it based solely on what I've written here.  These are just reminders if you've done it before and know to what all this is referring.

To transfer data from the /data/mcfuser directory, you can ssh into bl831:

ssh -l mcfuser bl831.als.lbl.gov "download holton semet_2_E1_035.img" | tar xvBf -

Here files are always transferred in chronological order (of collection), and any new files will be transferred as soon as they appear on the disk. The word "holton" means to download all files containing the string "holton", so use your data directory name here. The word "semet_2_E1_035.img" means to only send files that occur after semet_2_E1_035.img. This is useful if your first attempt at a download dies and you want to start the second transfer where the first one left off.

If "semet_2_E1_035.img" is omitted, then all files containing "holton" in their pathname are transmitted. If "holton" is omitted, then only newly-collected files are transmitted. Therefore, only use "download" with no arguments before you start collecting data.

NOTE THAT THIS MEANS YOU CAN BYPASS YOUR MAC's OR PC's HARD DISK. Simply mount the scratch disk using the normal samba method. Then in your terminal window cd /Volumes/xscratch1/yourdirectory and then type the above ssh command and the data should be transfered directly to the scratch disk.
On the computer on the way right, graphics2 (make sure the KVM switch is set so you are looking at the computer you think you're on, see the box with lights to your right), you can type burn.com and get directions on backing up various directories, file types, skipping certain directories, types and putting it all on DVD.  It makes 2 DVD's at a time and also prints labels.  Takes about 40 minutes to burn two fullish 2xDVD's.

Have you tried James' sendhome script?  Very convenient.  Type:

sendhome /data/mcfuser/myimages/oldest_image_to_send username@msg.ucsf.edu:my/image/directory

and after entering your password you should be good to go.  If you want to pick up where it left off, just enter a specific image to start from and it will send all images more recent than that one.  You can also bring a laptop with a big drive (internal or firewire) and plug into the DHCP network connection and copy files over that way.  There is an iMac there, so you could just bring the external firewire drive if you fancy.

You are in the very backyard of the Elves suite. So they'll do a lot for you, if you like, generally using mosflm to give you collection strategies.  Get thee to a working directory, type "Elves" and the path to your starting frame.  They should ask you stuff from there.

For you UCSF people, I'm our local Elf (contact) so it's available in /public/apps/bin on the SGI machines. Remember to set up any environment elves might be needing using the prepare scripts (i.e. ccp4, solve, etc.) or else Elves will try to download ccp4 for you.  You don't want it to do that.

You can use multiple processers on the crush cluster.  
ssh crush
and then launch your processer jobs there.  I don't think you can do the graphics stuff there, like the initial indexing with mosflm.

Some older frames may require an additional keyword for mosflm if you are running manually:

           PIXEL 0.1024

This is to get it to know how big the detector really is.

Denzo is working on 8.3.1 data, now.

The best way to make this work is go to any one of crush01 to crush06 and type:

 Disclaimer:  The information represented in this document is true to the best of my knowledge, including statements about your personal hygiene, your freakish appearance, and the proximity of your ancestors to semi-literate cave-dwellers from an evolutionary standpoint.  Things at ALS 8.3.1 change rapidly, however, so there are some reference dates for when various paragraphs below were known to be true, but always be aware that at the time of your viewing this document, there may be new better ways of doing things, and some of these old instructions may not be recommended or perhaps no longer even allowed or functional.  I keep these notes mostly as a reference for myself that I am happy to share with others, but be advised that I am not the beam line operator, I am not responsible for your actions at the beam (that would be you yourself), and as far as I know James Holton has not checked this page for accuracy (i.e. this is not an official ALS page). So I think these tips: are helpful, will generally work, can get you out of an unproductive jam at the synchrotron, etc., but they are no substitute for knowing and understanding what you are doing, and getting the proper help when needed.  James posts his number at the beamline.  And after all that negative sounding junk, best of luck and may your crystals diffract to 1.4 angstroms or better.