
Below will be found the documentation for operating beamline X12-C. The documentation for the running of data-reduction programs like denzo, Mosflm, or XDS are available elsewhere, though some Denzo hints can be found below.
If you encounter problems with the beamline, be sure to read Beamline Troubleshooting. You should take the time to familiarize yourself with the troubleshooting documentation before problems occur.
Life at the NSLS:
There is a nice (and very complete) description of
almost everything you might need to know about how to get along on
Long Island and at BNL, provided courtesy of the BNL Public Affairs
group.
All people who do work at BNL must have an "appointment" with
the Lab. This will be a "guest" appointment and you will arrange
it through the NSLS Users' Administration office. If you are
not a US citizen, the process may be more complicated than if you are. The
Biology Department User Coordinator's name, phone number, and
E-mail address can be found on the front page of beamline documentation if
you need forms or advice.
A second item of business is your Experimental Safety Form.
You will already have given us information about the safety aspects
of your experiment in the application form. The Biology Dept. User
Coordinator will help you to submit a form; please be sure it's
done in advance.
You can make your own arrangements in advance for housing with the BNL housing office (phone number: 631 344 2541). They're pretty convenient and inexpensive; they can be paid for with a credit card. You have
a responsibility, once reservations have been made, to use them or
cancel them. If you fail to cancel unused reservations, you'll
have to pay.
Visitors are strongly encouraged to arrive for their
visit to the NSLS early enough to spend some time checking crystals,
getting training, assuring that all tools are in place, etc.
An arrival at the lab of 3 PM or so will allow time to obtain help if
necessary from the beamline technician before he goes home, and to get
the NSLS
training completed.
After your arrival at BNL you should go to the NSLS Users'
Administration office to register. To find this office, enter the
front door of the NSLS and climb the stairway behind the doorway to
the left. After filling out various registration forms, you'll get a
film badge and be instructed to watch a video tape about safety. We
reiterate from above that we encourage you to come
early. You could be taking data by 9 AM if you plan ahead.
At any hour of the day or night you can obtain your safety training
through the personnel in the NSLS control room. They will give you a
blue card-key that will admit you to the
experimental floor. In the worst case after an early arrival one
will have time and materials to make preparations or repairs that
might have wasted hours of beamtime the next day. In the best case,
one can go to the beach. Note: You do not need to
register at the NSLS users office to begin your experiment if you have
the safety training! The registration can be performed at leisure
during the first day of running. Come straight to the beamline on the
first morning.
Things that typically go wrong include having freezing loops
mounted at the wrong height, having some crystals die so others need
to be soaked, or not having the right goniometer-head key.
We remind users that the principal factor that contributes to lost
beam time is crystals that degrade during transportation to BNL. Take
We have our own laboratory right at the beamline. You may
manipulate specimens, think quietly, or do computing there (there's a PC). There is a coldroom nearby in the building
for your use. You may have food at the beamline, but please
take no food into the laboratory -- we're on shaky ground
with the safety committee as it is. There is a key for the
laboratory; ask where it is and keep it locked when you leave for an
extended period.
The color TV monitor at the beamline tells you things about the
operation the ring. Channel 9, the most useful channel, has a
continuous message regarding the status of the x-ray ring. It's Red
during injection, Green during ramping, and Blue during operation.
You can read the present current and the 1/e lifetime, as well as some
messages about operation. When calamities occur, up-to-date
information about repairs to the synchrotron can often be found on
channel 2. Channel 11 carries the weekly schedule
for ring operations.
At the end of your visit, before you leave BNL, please
submit an end-of-run form.
It's also crucial to the continued funding of the facility
that you submit an abstract
describing your result when we request them (typically once a year).
Operation and troubleshooting of the data collection software
depends on the detector (B4,B1) being used.
The detector actually is made up of a 2x2 array of 1K CCD
detectors. Each detector is controlled by a PC running Linux. Their
nodenames are lsx12i, lsx12j, lsx12k, and lsx12l. On one of the
beamline computer monitors should be four shell windows, each of which
is a telnet session to one of the PCs. The username for the PCs is
"det", we will give you the password. The only thing that should be
run on the PCs is a progam called "server". After starting "server"
and seeing some information scroll by, the program should wait with
"Accepting service request". At that point the data collection program
"CBASS" can be started.
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Summary of data-collection procedures
Written by Ruiming Xu and Margaret O'Gara START UP THE SOFTWARE:
B4 software summary
This is intended as a summary of the critical software aspects of the
B4 detector. More details concerning the B4
are available.B1 software summary
The single-celled CCD detector is controlled by a Windows PC that
starts up the detector-control software at boot time. Users almost
never need to touch this computer. More
details concerning the B1 are available.
After locating a disk with enough space, create a top level directory with a name that is desciptive of your institution, PI, or project. Move into that directory and type "cbass&".
After a few seconds the CBASS GUI will pop up with a message "downloading please stand by" in the scrolled white window at the bottom. After downloading is complete, a white shell window will pop up in the upper right hand corner of the screen if you are using one of the CCD detectors. This window contains the output of a "server" program running on an sgi that will service requests from CBASS for detector data. The "server" running on the sgi will then communicate with the "server"s running on the PCs to get the data. The text scrolling by in the white server window is informational and there is no user-interraction directly with that process.
ALIGN THE BEAM
SET THE WAVELENGTH:
by clicking on "Realign". Be sure to have
shutters open before issuing realign!! Alignment should take a few
minutes. It is finished when no text field in the OptiX window is
green. If you wish to change the wavelength before collecting data,
then change the wavelength before doing the realignment.
and energy (keV). If you want to go to a specific wavelength or
energy, click the corresponding text field in the first row, type in
the desired number, hit RETURN key (always enter RETURN key after
inputting data when you are working with CBASS or OPTIX!!!). Then
click on "MOVE to TARGET" button.
CENTER A SPECIMEN:
"smv" is a program that will automatically display the most recent
image that has been recorded by the detector. We
HIGHLY RECOMMEND that you keep it running
at all times and that you LOOK AT YOUR DATA AS THEY ARE BEING
MEASURED.
From a shell window on one of the workstations other than the one that
you're using to run the data collection software, type "smv&" That will
bring up a display program written by Marty Stanton at Brandeis University.
Do the following to get it to display images automatically:
Choose a starting orientation for your crystal that you like and then
press the Set Relative Zero to Current Position button in the
lower left hand section of the CBASS GUI. This should not be done
again with this crystal.
We suggest that you take test exposures in the Det level so
that you can take advantage of the "fake dark" feature. When faking
dark images, the software will use or take 2-second darks rather than
requiring dark images of the same duration as the exposure. This can
save time if you are varying the exposure time while screening
crystals.
COLLECT DATA:
We recommend that you use our Strategy program to predict the most
efficient data-collection range for a sweep of data or pre-orient the
crystal. Suggestions for how to do this can be found below. However....
SOPHISTICATED MONOCHROMATOR CONTROL:
TO RUN "STRATEGY" OR TO PRE-ORIENT A CRYSTAL - DENZO Indexing with
CBASS See also the detailed description of
Orient below. The instructions below are intended to minimize
errors. Experienced users will find that there are shortcuts. We
recommend that you cut no corners until you have become familiar with
the interplay among the images, crystal parameters, programs, and
files involved in this process.
PAUSING DATA COLLECTION
ABORTING DATA COLLECTION
Connecting Your Own PC to the Network:
Users may connect their own PC to the laboratory network through the DCHP server by following the instructions available on the NSLS web-site. The computer must be registered by filling out a web-based form within 30 minutes after the computer has connected to prevent the network port from being deactivated.
Specimen Cooler:
The FTS cool air system is no longer in regular use.
If you have an application that requires this system in place of the
Oxford cryogenic cooling system, please let us know in advance of your arrival
either through your beamtime request
or by direct e-mail to the technical staff.
A document that describes how to operate the
controller for the Oxford Cryostream liquid-nitrogen-based cooler is
kept in the file cabinet at the beamline, and some troubleshooting information is available on the web. One can find
a brief description of how to get the unit going
below.
Nitrogen Supply:
There is a 50 liter dewar located inside the hutch from which the Oxford system
uses liquid nitrogen. When full, this dewar will last for 48 hours of continuous operation.
This "use dewar" is equipped with an auto-fill system (the "blue box," located in the coldstream equipment cart) supplied by a larger dewar outside of the hutch.
The controller should always be left in the "AUTO" position unless a staff member tells you otherwise.
We suggest that you put your crystal onto the goniometer head with the
diffractometer set to the position equivalent in Eulerian angles to
omega = 180 and chi = 45. In this way the crystal axis will be
pointing 45 deg. downward, and it will be perpendicular to the stream
of cold gas coming from the Oxford system. One can do this from the DET level or with the
manual-control pod. The settings on the kappa goniometer that are
equivalent to these Eulerian settings are omega = 160 and kappa =
60.
It may be necessary to withdraw the cooler from the position described
above to mount your specimen -- bring it back no more than is
absolutely necessary, then put it back as soon as the specimen is in
place. When very high resolution data are being taken, there
may be a shadow of the cooling snout on the detector. It is possible
to remount the cooler slightly upstream, but that should be done by
the beamline staff. Think about choosing a shorter wavelength.
Goniometer Heads and Height of Freezing Pins:
The FAST diffractometer has no z-axis adjustment possible. One must
use a goniometer head with a built-in adjustment. The distance from
the flat surface on the phi axis on which the goniometer head is
mounted to the crystal position is 64mm. Other useful distances are
shown in the diagram to the right and the one below.
We use Huber arc-less heads, which have a pretty long adjustment.
The range of distances from the top of the platform on these heads to
the specimen position is approximately 21 to 26.5 mm. For greatest
success in centering crystals, shoot for a distance of 23 mm. from the
platform to the crystal.
Others like to use the proprietary Hampton Research Company
system. We own one of their magnet assemblies, which can be placed on
the top of a goniometer head. Important distances are shown in the
diagram.
If you intend to bring your crystals pre-frozen, you should take
very seriously the problem of making absolutely certain that
you will be able to position your crystal perfectly on our
diffractometer. Please bring a pin/top-hat of identical dimension to
that used for your pre-frozen crystals for alignment of the goniometer
head, etc.
There is a pair of shutters connected with the diffractometer. The
diffractometer has a solenoid-driven shutter, the status of which is
indicated by the Beam-On / Beam-Off lights right on the
diffractometer. In addition there is a pneumatic shutter upstream of
the diffractometer, mounted behind a large copper-plate x-ray shield.
The internal timing of the operation of the machine is intended to
have the very fast pneumatic shutter actually controlling the
exposure. During normal operation, both are activated by Shutter-Open
/ Shutter-Close commands to CBASS.
Manual Control of Diffractometer:
The manual-control pod in the x-ray hutch allows one to drive the
diffractometer by hand. It often pays to press the [clear] button
when the device is picked up, just to empty its little brain. There
is the possibility that the readout will be garbled although the
commands work correctly. A beamline person can fix it for you.
There are two useful modes:
Crystal-Visualization Microscope:
There is a video microscope mounted above the crystal position,
viewing vertically downwards. There is a video monitor in easy viewing
overhead at the diffractometer, and a slave outside. There are
electronic cross-hairs to show the position of the rotation axis (single
vertical wire) and the x-ray beam (double horizontal wires, between which
the x-rays can be found). Illumination comes from a fibre-optic lamp suspended
above the specimen. Note that it rarely helps to
turn the lamp up above its lowest setting -- if it seems not bright enough,
put it closer. Uninitiates are not encouraged to adjust the cross-wires,
nor to try to focus the microscope. When in doubt, adjust the crystal to
be stationary during rotation and ask your host for advice.
Baby Pictures:
One can use the video capabilities of the Indys at the beamline to
take home a picture of your crystal:
Automatic Display of Images:
Images are displayed using a program called "smv". More information can be found
above.
Remarks on MAD-data collection:
For other edges and PostScript plots of other edges, see Ethan
Merritt's data about anomalous scatterers: numbers and graphs .
Entering Collect Runs with a Sweeps File
When a data collection run starts, a "sweeps.dat" file is generated
that records the information in the "runs" table of "collect". An identical
file under a name that embeds the start and end positions is also generated.
This file can be edited if needed and read back into CBASS from the
"Files->Read" menu. This feature is useful for restarting/continuing
a run that was interrupted for some reason. When editing the file there must
be a directory entry but it is not used by collect. Collect only considers
the file prefix and the current directory. The directory field is used
when processing with "onebutton". You must be very careful not to
alter the format of this file while editing.
Look at the B4
documentation for some comments -- the point is that we pretend that
this is a MAR300, but with 2/3-sized pixels. To do so, the detector distance to be specified in the auto.dat file should be 1.5 times the physical distance. The auto.dat file generated from the CBASS program should have done this correctly.
Files for operation of denzo for the B4 camera are available: auto.dat.B4, refine.dat.B4, scale.com.B4, scanall.com.B4. They contain some internal
documentation (!!) that we recommend you study. Also is a file strat.inp.B4 for operation of the X12-C
Strategy program, the command for which is "strategy".
Visit HKL Research's web-site for a searchable list of Denzo keywords and an on-line manual.
How to use it:
Typically (we strongly recommend this) one would create a
sub-directory below the data directory for the data reduction.
There are two ways to use the program. Both require a "peaks.file"
resulting from running HKL's xdisp program (formerly
INST_something). If you are currently taking data
, then copy the files auto.dat, refine.dat, and sweeps.dat,
that have been generated for you by CBASS, into your processing
directory and use option 1.
Option 1) If you already have auto.dat and refine.dat in
your processing directory:
type : onebutton (return key)
Running "onebutton" in this fashion requires "auto.dat" and
"refine.dat" command files that are good enough to index the image
that was used to generate "peaks.file".
Option 2) Uses a MAR image with correct file header
info. (The ADSC MAR software usually takes care of this for you)
type : onebutton [mar image filename] (the one peaks.file
was generated from)
In this case, the software should generate a pretty decent
auto.dat program from this. However, if it is not good enough to
index the image, you may want to get out of onebutton, make
adjustments to "auto.dat" and then re-run onebutton as in option 1
(i.e. just type "onebutton").
In both cases, a file that CBASS generates to record data
sweep info (sweeps.dat) is also used but will be generated if you do
not have one. This file may be useful when users set up the data
collection program to take multiple data sweeps, like when they're
using the Friedel Flip to measure Bijvoet pairs, or doing a
MAD experiment.
Given the above, "onebutton" will do the following:
1) Index and refine the image specified in auto.dat.
2) For each data sweep requested in the data collection program:
Generate command files, named "auto#n.dat", where "n" is the row
number in our data collection window. Each will contain the refined
parameters from the autoindexing run, such as distance and beam-center
coordinates. At this point onebutton will prompt the user for more
subjective parameters, including the spot diameter, mosaic spread,
outer resolution limit, etc.
3) Run denzo with these command files while displaying a continuous
graphical analysis of Denzo's output.
4) Generate textual log files for some of the graphical data.
Note:
You may pause and restart anytime before the last image is
processed. To restart after all images have been processed, you should
quit and re-execute the program.
Feel free to Download
onebutton. The distribution contains everything you'll need
including a few image files. Be sure to read the README file included
in the distribution.
If you have comments, questions, complaints, etc., please contact:
OPERATION OF THE IMAGE-VIEW SOFTWARE
TAKE TEST EXPOSURES:
command to write a .sav file, a denzo command file, and a
MOSFLM command file. This provides almost complete documentation of
your experiment. (You may find them handy later on.)
You can pause data collection at anytime by pushing the Pause
button in collect. After pushing the button, its label will change to
Continue. Pushing Continue will resume data collection.
You may use this feature to perform a Realign in OptiX
during data collection or after a fill by performing the following steps:
You can abort data collection by pushing the Abort
button in collect.
You must not abort data collection
if you are in the process of doing a wavelength scan!!
Go Back To Table Of Contects (TOP)
Odds and Ends of Operation
26 October 1994
*A good, quick rule of thumb when using Hampton pins is that a pin broken off on the second "notch" will be about the right height to fit on our machines.


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DENZO Hints
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Onebutton - BNL's Automatic Graphical DENZO Processing Tool
How "onebutton" works:
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Last modified 9 April 2002 by Protein Crystallography Web Master