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The National Institutes of Health (NIH),
through its National Center for Research Resources (NCRR) Program,
funds a facility, called MacCHESS, to support macromolecular
diffraction at CHESS. Briefly described below are new changes,
improvements, current hardware and software configurations and
ancillary equipment. MacCHESS supplies specialized support equipment
and expertise for these studies. Access to this support facility is
requested using the standard CHESS Express Mode or Extended Access
Proposal form. See the section on "Allocation
of x-ray beamtime" for more information.
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Small-Angle X-Ray Solution Scattering (SAXS)
at MacCHESS. Protein envelope reconstruction
HOWTO. |
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A "click to center" Java-based
graphical user interface employing a high quality digital video
camera is available for rapid centering of crystals. Fully
automatic centering is now also possible, using the GUI's "Auto
Center" button and the XREC software package. |
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ADSC
Q-270 detector at the F1 station |
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A new ADSC
Q-270 detector is now available for use at the F1 station. This
is the latest development from ADSC; it utilizes a new low-noise
CCD chip for improved performance with weakly diffracting
crystals. As its name implies, the Q-270 has an active area 270
mm square, over 50% larger than the Q-210 detectors installed at
A1 and F2. In pixels, the dimensions are 4168 x 4168 (2084 x
2084 in binned mode). The readout time is about 1 second,
similar to the Q-210 and considerably faster than the older Q-4,
which was previously the only type of detector available at F1.
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In testing at
CHESS, data from the Q-270 were similar in overall quality to
data from other ADSC detectors, perhaps a little better for weak
reflections. Data are readily processed with HKL2000 and denzo, DPS, mosflm, or XDS. Users at F1 can
choose to use either the Q-270 or one or both Q-4's; switchover
is quick and easy. |
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Marian Szebenyi
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A
facility for cryocooling crystals under pressure is now
available at MacCHESS. This technique, developed in the Gruner
lab, was reported in (Kim et al., Acta Cryst. D61, 881 (2005)).
It involves mounting a crystal on a special pin, pressurizing
it, cooling to liquid nitrogen temperature, and then releasing
the pressure while keeping the crystal cold. The method can
allow successful cryocooling using little or no penetrating
cryoprotectant, and can produce cryocooled crystals of better
quality than the usual cryocooling method. In addition,
pressure-cryocooling can act to stabilize a single conformation
of a bound ligand, hence making it visible in an electron
density map (Albright et al., Cell 126, 1147 (2006)). It is also
possible to apply the method to samples in capillaries, both
solutions and crystals mounted, or grown, in capillaries.
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Having
constructed and tested the necessary equipment at CHESS, we are
now making pressure-cryocooling available to the user community
on an experimental basis. Some important details: |
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Pressure-cooling
will not make a crystal better than it is at room
temperature; it only reduces the damage due to cryocooling.
Therefore, it is advisable to be sure your crystal diffracts OK
at room temperature before trying pressure-cooling. |
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Because the mounting
process for pressurization takes a longer than
the standard mounting process, the crystal must be coated in oil
to
prevent dehydration. Hence, crystals that dissolve in oil will
not work
- we suggest you check on this ahead of time. |
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The process starts
with a room-temperature crystal; we cannot take a
cryocooled crystal and pressurize it. |
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The crystal handling
involved is a somewhat tricky, so MacCHESS staff will
carry out the pressure-cooling procedure, although you are
certainly welcome to assist and observe. |
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We need some lead
time to set up the pressure-cooling, so you must make
arrangements ahead of time if you want to bring unfrozen
crystals along on a CHESS visit and give the technique a try.
Once crystals are pressure-cryocooled, the pressure is
released and they are handled like any other cryocooled
crystals. Hence, they can be stored in liquid nitrogen and need
not be used immediately; you do not have to wait for a CHESS run
to try the technique. |
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If you
have some crystals that freeze poorly, and you would like to try
this new technique, or if you would just like more information, contact
Marian
Szebenyi,
Chae Un Kim,
Irina Kriksunov |
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Faster and better data
collectionat the F2 station: |
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Flux down the collimator has been
improved, particularly at low energies, by installation of a
longer in-vacuum focusing mirror, removal of some absorbers in
the beam upstream of the hutch, and replacement of the beam pipe
in the hutch with a helium-filled, better shielded, model. A
group that recently collected data at the Zn edge (9.6 KeV)
reported a 20-30% improvement in X-ray intensity over an earlier
visit. Another group was able to get sufficient anomalous signal
at 7.1 KeV to successfully perform sulfur SAD phasing. At the
optimum energy of about 13 KeV, high quality monochromatic data
may be collected, albeit with
exposure times longer than those for A1 or F1.
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Energy drifts have been reduced,
due to increased beam stability in the present filling mode and
to better thermal control for monochromator box components. New
software makes it easier to perform energy calibrations when
needed.
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Data collection facilities are on
a par with the A1 and F1 stations: the goniostat incorporates an
air bearing to allow rapid, precise spindle rotation, the X-ray
detector is an ADSC Q-210 CCD with 1-second readout time, a
convenient and reliable crystal centering system is in
place, and new Opteron computers with a 2 TB RAID system
attached are used for data collection and processing. A variety
of phasing and structure solution programs are available. |
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Marian Szebenyi
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A-1
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ADSC Quantum-210 CCD
detector (four 2048x2048-pixel modules), monochromatic radiation
at 0.976 A. Currently crystal-to-detector distance can run
from 99 mm to 445 mm. |
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F-1
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ADSC Q-270 CCD detector, dimensions are
4168 x 4168 (2084 x 2084 in binned mode); monochromatic
radiation at 0.916 A.
Currently crystal-to-detector distance can run
from 95 mm to 900 mm. |
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F-2
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ADSC Quantum-210 CCD
detector (four 2048x2048-pixel modules); MAD 0.77-1.60A.
Currently crystal-to-detector distance can run from 53 mm to 569
mm. |
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F-3 |
ADSC Quantum-4 CCD
detector (2304
x 2304 80-micron pixels), somewhat slower readout time but
produces excellent data. |
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Image plates are no longer
routinely used for macromolecular crystallography data at CHESS,
but are still available for unusual experiments, e. g. those at
very high energies where the usual phosphor coating on CCD
detectors has poor sensitivity. Fuji image plates (8" x 10",
2048 x 2500 100x100 micron2 pixels, dynamic range 104,
90-second readout time) and a BAS2000 scanner are available. For
more information on use of image plates, contact |
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Bill Miller
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Pixel array detectors (PADs) are
being developed by the Gruner group, for several different
purposes. These are currently small devices, 128 x 128 pixels or
so, but have a very short readout time and very low point spread
function. They are occasionally available for special
experiments through collaboration with local scientists.
For more information, contact: |
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Sol Gruner
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Single-axis goniostats
incorporating fast, air bearing-based, rotation stages with
approximately 1-micron runout are installed at all the MacCHESS
stations (A1, F1, F2, and F3); each is fitted with precise
stepping or piezo motors for centering crystals in the beam.
Other equipment needed for collection of oscillation data,
including a fast shutter, an X-ray collimator (100 micron
diameter is standard; larger sizes are available, also focusing
capillaries to produce smaller beams), an ion chamber to monitor
counts, etc., is also available at each station. |
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All
macromolecular stations have been equipped with new Cryostreams
700 series from Oxford Cryosystems |
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The temperature is
usually set to 100 K, but can be varied from 80 K to 400 K. The
systems can be programmed to cool down or warm up with a
specific gradient, reach certain set points and hold these for a
certain amount of time. The cold gas flow is variable and can be
set to either 5 or 10 L/min (turbo mode). For temperatures below
100 K the system automatically adjusts the flow to 10 L/min, for
temperatures above 100 K a flow of 5L/min is sufficient to
maintain the temperature within 0.1 K. The cold gas flow can be
positioned in many different ways, from vertical to horizontal.
Accurate alignment is being done using the three positioners at
the support stand with the aid of a nozzle alignment tool. |
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Ulrich
Englich
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HKL2000, a graphical interface to
Denzo, XdisplayF, Scalepack, and associated routines, is
available, through a collaborative arrangement with HKL
Research, on all the MacCHESS computers. All detectors in use on
MacCHESS beamlines are supported. |
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DPS/mosflm/CCP4,
version 2.03, for all detectors at CHESS. A tutorial on running
this package is available in the "Processing data" section of
these web pages. |
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Marian Szebenyi
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MacCHESS data
collection computers at each beamline have been replaced with
Linux machines. An additional two Linux machines are located at each beamline for data processing and
backup. More Linux computers and Alphas may be found in
the computer room, where two of the Linux machines (kaoline &
opaline) are equipped for 'stereo' graphical use. All MacCHESS
data collection/processing computers are linked via gigabit
ethernet. The Linux computers have a variety of data
processing software (see below) along with common
crystallographic software including CCP4, Solve, pymol, O and
SnB. |
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Apple Mac computers
are stationed at F1 and in the computer room for data
backup. Currently the Macs do not have a lot of crystallographic
software. |
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David
Schuller
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Each data collection machine has
a 2 TB RAID array attached.(/A1a, /F1a, /F2a). Data should be
written to the RAID array if possible for best capacity and
performance. Additional disks and a spare RAID array are
available in case of emergencies, and should be kept clear in
case their use is needed. |
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Users are welcome to bring their
own laptop or other computers to CHESS for data processing and
backup. IP addresses can be set up easily with DHCP, and static
addresses are also available. |
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MacCHESS supports IEEE 1394
(FireWire) and USB 2.0 connections on Mac and Linux. These
interfaces are also available on Windows machines supported by
CHESS. The Macs (macmac in the computer room and tarmac at F1)
also support FireWire 800 (IEEE 1394b) as does the Linux machine
kaoline in the computer room. |
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Data can be transferred from
CHESS to your home lab over the network.
CHESS/MacCHESS is connected to the Cornell campus network via
gigabit ethernet. Transfer speed to your home lab will vary from
case to case. CHESS has a firewall, so connections to CHESS from
outside are difficult. Consult your staff scientist if incoming
connections are necessary. |
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Tape drives are still available;
please contact MacCHESS in advance if you wish to use any of
these tape formats: 8mm (Exabyte 8500), 4mm (DDS 1-4), DLT4000,
Ultrium. |
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For a more detailed description
of data backup and transport, see Dave
Schuller's web page on bringing your data home
http://staff.chess.cornell.edu/~schuller/backup.html |
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David
Schuller
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