Categories of questions:
Q: Does IMCA have a web page?
A: Yes, it is located at http://www.imca.aps.anl.gov/
Q: What can be found on the IMCA web page?
A: The IMCA web page has information on the activities of the CAT
staff as well as a comprehensive Sector
Orientation Guide, the CAT Environmental
Safety and Health Manual, Staff contact information, and much more.
Why don't you go take a look?
Q: Is there reliable documentation for the Mar CCD and the software
that drives it?
A: Lisa has created a quick-reference sheet with the basic instructions
on it, as well as a troubleshooting sheet to help you handle things when
problems arise. The manual, such as it is, for the Mar software is online
on the data-acquisition computer.
Q: I am embarrassed. I have forgotten how to search and secure
the hutch I am using.
A: The search and secure procedures for all four of the IMCA sector
radiation enclosures is located in the beamline operation manual. Read those
instructions, and you'll probably be fine. If not, check with a staff member.
Q: How do I ship samples and reagents in and out of the APS?
A: If the samples are considered non-hazardous by the Department
of Energy, you may transport them by private vehicle. If any hazardous
materials--including liquid nitrogen or liquid or solid propane--are
involved, then you must ship the samples in and out via a common carrier,
usually FedEx. Instructions
are available for this type of shipment. Call Virginia
Brown at 630-252-0520 for details. If your samples or reagents are non-hazardous,
a simpler set of instructions apply. See the
next question for details about heavy-atom reagents.
Q: How does IMCA-CAT handle non-radioactive heavy-atom reagents?
A: Any sample that has been pre-soaked in a heavy-atom reagent, except
dimethyl mercury, tetraethyl lead, and tetramethyl lead, is permitted
and may be brought in under the rules described above. If you wish to do
a soak on-site, and the specific heavy-atom reagent is considered non-hazardous
under Department of Transportation
guidelines, then you may bring it into the facility in a private vehicle.
If the reagent is considered hazardous by DOT, then you must ship it via
common carrier through building 5 by the method described in the instructions. IMCA intends to develop a small stock of
non-radioactive heavy atom reagents on site, but we have not done so yet.
Watch this space for details. IMCA-CAT has developed a standard
operating procedure for performing heavy-atom soaks onsite; you must
follow it if you want to do a soak at IMCA-CAT.
Q: How does IMCA-CAT handle radioactive heavy-atom reagents?
A: Any sample that has been pre-soaked in a uranyl or thorium reagent
is permitted and may be brought in under the rules described above. This
is because the amount of radioactivity involved is lower than that defined
in table 02-3, Chapter 5-02 in the Argonne
Environmental Safety and Health Manual as requiring Argonne's special
attention. Currently we cannot accommodate doing radioactive soaks
onsite. We will develop that facility soon.
Q: Can we ship samples in or out in propane "popsicles"?
A: Yes, but currently the procedures for shipping them out are rather
cumbersome. Argonne Environmental Health and Safety has ruled that solid
propane, even in the extremely small quantities used for these popsicles,
is hazardous. After substantial effort the APS developed a set of rules for transport of small quantities of reagents
like propane, and you are allowed to ship samples in propane provided
you follow these rules. Note that the DOT exemption embodied in these rules
applies only to samples being shipped between the APS and your home
institution; if, by contrast, you want to cover shipments between two of
your own corporate sites, you'll have to work directly with DOT to get a
similar exemption.
Q: How do we control the beamline components?
On the insertion-device beamline there exists a simple beamline graphical user interface program called "imca17id" (named for the CAT, the sector number, and the beamline type). Type the name of that program while logged on to thalia, and you'll get a GUI interface with which you can change the monochromator energy, the slit sizes, and other facilities. From it you can invoke optimization routines that will give you maximum flux onto the sample.
There exists a more feature-rich but slightly less user-friendly graphical user interface package called "mxgui" (named for the MX package, above which these GUIs ride). This GUI is intended primarily for staff use.
Beamline controls can also be accomplished through a few epics screens
and a command-line program called MOTOR, which Bill Lavender wrote and is
available to you. The best descriptions of motor and the mx library, which
it uses, are found at http://www.imca.aps.anl.gov/~lavender/mx/
.
MOTOR runs on all our machines, but you'll probably be running it from `terpsichore',
which is the O2 right next to the NT machine. MOTOR has a straightforward
syntax. It lets you move everything around with simple commands, e.g.
motor> move lambda 0.9765
motor> move energy 12696
motor> mabs energy 12696
do exactly the same thing, namely, change the monochromator theta to a theta
corresponding to an energy of 12.696 KeV, i.e. 0.9765 Ångstroms. If
everything is working properly, it will automatically change the other objects
that need to be moving simultaneously, i.e. the goniostat table heights,
the omega and chi adjustments of the second crystal in the mono, and so
on. In practice what you'll use it for is
Q: I am not getting any diffraction data on the CCD! I was getting
data just a minute ago!
A: IF you have entered the hutch between the time you were previously
collecting data and now, then you may have:
Go into the motor program and run `scan slow1k'. If you are
not getting any counts in the ion chamber, make sure the shutters are
open and then go into the hutch and make sure that you have not moved the
ion chamber.
If you are getting counts in the ion chamber, and you are still not
able to see a diffraction pattern on the CCD, then you should:
If you still are not collecting any data, then:
| Name | APS Office | Pager |
| Lisa Keefe | 630-252-0544 | 630-314-0544 |
| Andy Howard | 630-252-0534 | 630-905-0534 |
| Irina Koshelev | 630-252-0523 | 630-905-0523 |
| Qing Ma | 630-252-0529 | 630-314-0529 |
| Carin Stamper | 630-252-0525 | 630-314-0525 |
| Katie McCarthy | 630-252-0530 | 630-314-0530 |
Q: How are you doing fluorescence scans, and energy selection?
A: We have a simple Bicron fluorescence detector that we mount in
the horizontal plane, perpendicular to the incoming beam. It takes about
thirty seconds to set it up. We measure the fluorescence signal from it
using the scan facilities built into the "Experiment -> MAD"
part of the imca17id GUI. imca17id has a built-in graphing
interface (using GNUPLOT-- nothing fancy, but it works) so you can stare
at your scan. Once the scan is completed, imca17id provides you with
a button labeled Calculate f', f". If you push it, the package
will invoke CHOOCH to perform the appropriate calculations. The instructions
for using this implementation of CHOOCH are found at the beamline. Once
you've identified your peak and inflection point the energies associated
with them, as well as the f' and f" values at those points, are recorded
on the imca17id MAD screen. You can specify low-remote and high-remote
energies on the screen, and the program will interpolate values of f' and
f" for those energies as well.
Currently it's necessary to transfer these energies by hand to the data acquisition GUI for the Mar system.
Q: What kind of goniostat does IMCA-CAT have on its insertion-device
beamline?
A: It is a Mar system with one crystal-rotation axis (phi) and a
computer-controllable sample-to-detector distance. This system, known as
"Mar base", is found on almost all Mar installations worldwide,
both at storage rings and in home labs. It has built into it a pair of slit
assemblies and ion chambers, enabling users to adjust the base to maximize
intensity through the chambers for a given opening size of the Mar slits.
The phi axis can be manually spun and then operated from the computer, provided
the user remembers to re-set the motor angle to zero (the fiducial position)
after manual adjustment. The Mar phi axis has a generous z-translation capability,
so you are not severely restricted in the position of the sample relative
to the base of the goniometer head. Any distance between about 60 and 75
mm can be accommodated, but 70 is probably optimal. We have several spacers
that replace the normal goniometer-head magnets, each providing a different
height adjustment. This provides additional flexibility in the mounting.
Q: What kind of goniostat does IMCA-CAT have on its bending-magnet
beamline?
A: It is a Mar system with one crystal-rotation axis (phi) and a
computer-controllable sample-to-detector distance. This system, known as
"Mar base", is found on almost all Mar installations worldwide,
both at storage rings and in home labs. It has built into it a pair of slit
assemblies and ion chambers, enabling users to adjust the base to maximize
intensity through the chambers for a given opening size of the Mar slits.
The phi axis can be manually spun and then operated from the computer, provided
the user remembers to re-set the motor angle to zero (the fiducial position)
after manual adjustment. The Mar phi axis has a generous z-translation capability,
so you are not severely restricted in the position of the sample relative
to the base of the goniometer head. Any distance between about 60 and 75
mm can be accommodated, but 70 is probably optimal. We have several spacers
that replace the normal goniometer-head magnets, each providing a different
height adjustment. This provides additional flexibility in the mounting.
Q: What is the actual control program for the Mar, and do you
have a manual or training procedure on it?
A:The data acquisition is done by marccd, which runs on the
Linux computer closest to the hutch (charybdis). marccd is responsible
for crystal manipulation, image viewing, and acquisition of data sets. It's
also used to characterize the diffraction patterns: it has graphing facilities
to let you overlay resolution circles and the like over the diffraction
patterns. There is sketchy documentation available online on charybdis at
~marccd/documentation. Christine Muchmore has recently improved that documentation
substantially, and a copy of the new version is at the beamline.
Q: Is there data strategy software built into the Mar code?
A: No. HKL2000 and D*Trek provide this capability, and at least the
HKL2000 version works well with Mar data.
Q: What is the data format of the Mar images?
A: Each image file consists of a TIFF header, a crystallographic
header, and the 16-bit image data. The files are not by default compacted
in any way, but it is easy to use a standard compression program like "compress"
or "gzip" to squeeze the files down. The contents of the crystallographic
header are documented. By default the images
are dark-current subtracted, spatially corrected, and sensitivity-corrected
before being written to disk. Under special circumstances some of these
corrections can be disabled; check with the staff for details.
Q: What are typical exposure times on the Mar CCD systems?
A: On the insertion-device line with no attenuation, the following
numbers apply: For good diffractors, 0.5 - 2 sec is sufficient. Mediocre
diffractors require 2 - 8 sec; weak diffractors require 8 - 30 sec per image.
On the bending-magnet beamline you should probably quadruple these numbers.
Q: How far back should we set the detector to collect data?
A: For 1 Å radiation a good rule of thumb is about 0.95mm *
a, where a is the longest effective cell edge in Ångstroms. Thus for
a 100 Å unit cell you should set the detector at 95 mm. For longer
wavelengths the reflections are spread out more, and you can reduce this
linearly by the wavelength. Thus for 1.5 Å radiation you can collect
data on a 150 Å unit cell at 95mm.
General Questions:
Q: Does an interconversion program exist to facilitate going from
one detector image format to another?
A: Yes; it's called imageform, and it runs both on the SGI's
and on the Linux boxes. It can read any of about fifteen data formats and
write any of about five data formats. Documentation
is available.
Q: Are there reasons to try multiple processing programs?
A: Depends on how much time you have to fiddle with it, of course.
It's the staff's job to make careful comparisons among the various packages,
and we're now learning a lot by doing those comparisons. Whether it's worth
your time depends on your priorities.
Q: Some IMCA companies are using swappable disk drives to take
their data home. What data carriers can my company purchase that are compatible
with IMCA's computer hardware so that we can process our data at home?
A: We are currently using StorCase (formerly Kingston) DE100 series
carriers that expect a specific type of drive and drive holder. These systems
are described at http://www.storcase.com/dexpress/de100.asp and can be purchased
from CDW and other vendors.
The drives themselves that we recommend are mostly Seagate SCSI drives, including the ST150176LW (50 gigabytes). Many of these drives are available from CDW as well. The availability of these drives is currently in flux; we'll update this information shortly. Check for it here and at http://www.imca.aps.anl.gov/removable.html.
Questions about HKL2000:
Q: I've discovered a bug or a problem with HKL2000. I want to
ask the authors about it, and I want to warn other users that the problem
exists so that they can be alert to it too.
A: Send an e-mail to hkl-imca@anl.gov
outlining the problem. Anyone who has subscribed to this list-server will
receive your comment. Wladek Minor generally responds fairly quickly to
postings on this list-server, particularly if there's a good workaround
or if he can isolate the cause of the problem quickly. So it is a good mechanism
for reaching him for dealing with these kinds of problems.
X-GEN Questions::
Q: Is X-gen at 17ID pretty much the same as it's always been,
and do you recommend it over, say, HKL?
A: X-GEN has a snazzy GUI imposed onto it by MSI, although the single-program-at-a-time
version is fully functional and is updated at the same rate (or even slightly
faster) than the GUI version. So you can use either with no problem. We
can you some data to practice on beforehand if you want. So far we see few
substantial differences among data collected on the three packages (X-GEN,
D*Trek, and HKL2000). X-GEN's spatial correction stuff has had problems
close to the boundaries between the quadrants on the late lamented Bruker
system, but that got fixed, and in any case that detector is gone.
HKL2000 is a special case. I believe that it does a better job than either D*Trek or X-GEN if broad images are used. I doubt that it does a better job with three-dimensional data. So if you choose a stepsize that is wider than the rocking width, I'd recommend HKL2000; if you don't, I'd recommend X-GEN. Of course, many users are more or less well-acquainted with the user interfaces on the various packages, and with the experimental mind-set that these packages represent. Some users make their processing decisions based on those considerations rather than on considerations of the quality of the data output. We intend to continue to support at least two solutions: HKL2000, and X-GEN. We will support DPS once we understand it well enough to offer help to people.
Q: What is the format of the intensities output from the integration
portion of X-GEN?
A: The UREFLS file is a headerless binary file. Each record looks
like this:
typedef struct { /* structure type for a reflection observation:80 bytes*/
short obs_hkl[3]; /* indices of the reflection */
short obs_lpa; /* Lorenz/polarization/absorption
factor * 10000 */
short obs_ssq; /*scatt vector length squared * 10**4*/
short obs_xpred; /* predicted x position, pixels*10 */
short obs_ypred; /* predicted y position, pixels*10 */
short obs_region; /* detector partition (0-11) */
float obs_ii; /* integrated intensity */
float obs_sigma; /* variance of integrated intensity */
float obs_iunfit; /* non-shapefit intensity */
float obs_sunfit; /* non-shapefit variance */
float obs_ompred; /* predicted scanning angle position */
float obs_omob; /* observed scanning angle position */
short obs_gof; /* goodness-of-fit parameter */
short obs_shift; /* 16*(I(fit,kabsch)-I(fit,xyomega)) */
short obs_gama; /* rocking-curve correction */
short obs_xob; /* observed x position, pixels*10 */
short obs_yob; /* observed y position, pixels*10 */
short obs_widob; /* 8*(var(fit,kabsch)-var(fit,xyomega))*/
short obs_bgnd; /* average background under refl */
short obs_bgunfit; /* 16*(I(sum,kabsch)-I(sum,xyomega))*/
short obs_ncells; /* number of cells used in summing */
short obs_reflno; /* 8*(var(sum,kabsch)-var(sum,xyomega))*/
char obs_lowfrm; /* index of first frame integrated */
char obs_hifrm; /* index of last frame integrated */
u_char obs_chamno; /* chamber number */
u_char obs_runno; /* integer identifier of run */
short obs_frmint[7];/* background-corrected intensity
readings in individual "frames" */
short obs_flags; /* flags set during processing */
} OBSREF;
Q: When you use X-GEN to integrate data, do you do the scaling
in X-gen, or can the data be scaled in other packages?
A: X-GEN's scaling package is definitely usable and has been substantially
improved in the last two years. It is also possible to convert the UREFLS
file (see above) to a format that can be scaled in SCALEPACK. Similar conversions
are probably possible into other packages. Conversely, we now have a program
that converts the output of the integration portion of SAINT into a UREFLS
file. Using this, one can integrate data with SAINT and scale it with X-GEN.
Q: I am coming in to collect data from an institution that does
not have a user agreement in place with the APS. What do I do?
A: Ordinarily any researcher using the APS must arrange for his or
her institution to sign a user agreement with the APS. This defines who
takes responsibility if an accident occurs, and similar legal phenomena.
If you are coming in under the aegis of another organization (e.g., an IMCA
company) and that organization is willing to take responsibility for you
(e.g., they'll pay for the damages if you drive a fork-lift through the
beam-transport on our beamline and destroy the storage ring vacuum), then
then your home institution doesn't need to sign a user agreement. If you
don't have an affiliation like that or you want to more of an independent
player than that, then you probably should arrange to have your home institution
sign one. You can get the details, both about user agreements and about
user orientation and training, by looking at www.aps.anl.gov/xfd/communicator/useroffice/orientation.html
and the pages accessible from there. You can also call Liz
Stefanski, the APS officer in charge of these agreements, at 630-252-5503.
Q: I am about to publish a paper based on research done at IMCA's
beamline at the APS. What is the appropriate wording for acknowledgement
of IMCA and the APS?
A: Acknowledgement of the APS should be phrased as follows: Use
of the Advanced Photon Source was supported by the U.S.Department of Energy,
Basic Energy Sciences, Office of Science, under Contract No. W-31-109-Eng-38.
The APS also requests that one copy of each published manuscript be provided to the APS User Office, Building 401, Room B1154 as soon after publication as possible. The CAT staff will arrange for this; please provide the CAT staff with a copy of the article, giving it either to Lisa or Virginia.
The appropriate acknowledgement for IMCA-CAT is as follows:
Data were collected at beamline 17-ID (or 17-BM) in the facilities of
the Industrial Macromolecular Crystallography Association Collaborative
Access Team (IMCA-CAT) at the Advanced Photon Source. These facilities are
supported by the companies of the Industrial Macromolecular Crystallography
Association through a contract with Illinois Institute of Technology (IIT),
executed through the IIT's Center for Synchrotron Radiation Research and
Instrumentation.
Q: Do you have any old lysozyme or myoglobin data I could play
with to learn your system?
A: Yes. Contact the staff for details.
Q: How does IMCA-CAT handle experimental sample approvals?
A: At least five days before beginning experiments, each user group
should fill out the APS's Experimental Safety Approval form, available by
fax from us or from the APS, or by capturing the form off the APS website
at http://www.aps.anl.gov/xfd/tech/esafwww/esaf.html.
N.B.: The box at the top of the form that says "Classified Work
will be Performed" refers to government-classified experiments,
not company-confidential experiments. So unless you are actually doing what
the government considers classified work, do not check this box.
If you fill out the electronic form, it will automatically go to the right place. If you use a paper version, you can fax the filled out to form to us at 630-252-0521.
The decision that IMCA made at that point, and the one which the APS has so far agreed to, is that you can be fairly generic in section 4 on the APS forms. We recommend that you write something like
You also might consider using code numbers (e.g., merck603?) that can be directly related forward to the names you use as the sample prefix in data acquisition. That is irrelevant to the APS, but it might help you in relating your collected data to the contents of these forms.
If you have a large number of ligand studies planned, all associated with the same protein, you can treat all of them on one line, e.g.
. . . but if you would prefer one line per experiment, that is fine too.
The place the APS is adamant (appropriately) is that any departures from we call "normal macromolecular cryocrystallography" need to be noted under special conditions. Thus use of liquid propane or freon must be called out on the APS form.
After filling out the experimental safety approval form, be prepared to fill out a more detailed Experimental Sample Form that we in the CAT have drawn up. This form is available by mail from us; it's hard to fax, because it's 8.5x14". This form must be filled out prior to the beginning of data collection, and if you are not from an IMCA company it should be filled out several days before data collection begins. It's more efficient than the previous version in that you can put down information about all of your proteins on a single sample form rather than filling out one per experiment. The purpose of this detailed form is to provide specific information about your samples. It will not be made public; instead, the forms will be placed in a safe in the CAT Director's office, and the only people who know the combination to the safe are the CAT Director and the Associate Director. So if you provide sensitive information on these forms, you can be confident that it will not be released. Only in the case of a significant safety incident will the APS Environmental Health and Safety Coordinator ask to see the forms.
Q: I'm having a problem not covered in these FAQs. It's late at
night and I'm reluctant to wake people up. What do I do?
A: Please call a staff member. The continued operation of
the beamline is more important to us than our beauty sleep. The staff members
to call under these circumstances are listed here. We encourage you to page
these people rather than phoning them at home, but their home phone numbers
are available on the password-protected IMCA site.
| Name | APS Office | Pager |
| Lisa Keefe | 630-252-0544 | 630-314-0544 |
| Andy Howard | 630-252-0534 | 630-905-0534 |
| Irina Koshelev | 630-252-0523 | 630-905-0523 |
| Qing Ma | 630-252-0529 | 630-314-0529 |
| Carin Stamper | 630-252-0525 | 630-314-0525 |
| Katie McCarthy | 630-252-0530 | 630-314-0530 |
Questions, concerns or suggestions may be addressed to Lisa Keefe.