Remote Access Experiments at SSRL

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Remote Access Experiments at SSRL
Aina Cohen
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50 of scheduled users are collecting data
remotely
Aina Cohen
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Cost Comparison
remote data collection
onsite data collection (for a group from
Huntsville, AL)
Airfare 432.90 Meals 191.25 Lodging 195.0
0 Taxes 19.50 Rental car 148.00 Parking 24
.00 Total (per person) 1010.65 Total (3
people) 2735.95
Cassette Kit free (incl. cassette and
tools) Courier 200.00 (to ship dewar)
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SSRL Macromolecular Crystallography
Beam Line Operation and User Support Mike
Soltis Joint Center for Structural Genomics
Ashley Deacon
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Beam Line Operation and User Support

• Direct User Support - Scientific Staff
• Graeme Card
• Aina Cohen
• Tzanko Doukov
• Pete Dunten
• Ana Gonzalez
• Dan Harrington
• Irimpan Mathews
• Clyde Smith

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Beam Line Operation and User Support
Technical Support
Administration Lisa Dunn Computing Thomas
Eriksson Scott Talafuse Software Scott
McPhillips Penjit Moorhead Harcharan Singh Ken
Sharp Jinhu Song Hilary Yu
Electronics Renato Avelar Paul Ehrensberger Henry
Meier Vlad Vinetsky Mechanical Joseph
Chang Milorad Dragovic Mike Hollenbeck John
Kovarik John Mitchell Ron Reyes
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Beam Lines
BL12
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Beam Line Specific Information

• http//smb.slac.stanford.edu

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Centrally Managed
Identical Experimental Hardware Shared Spares
Pool Identical Software Shared Computational Res
ources Centrally Scheduled
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Advanced Detector Technology

• 3 Quantum-315 CCD Detectors
• 1 sec readout
• 315 mm x 315 mm
• 100 um pixel
• 3 MAR-325 CCD Detectors
• Low noise
• 1 sec readout
• 4 x 4 large active area
• Quantum-4 CCD Detectors
• 10 sec readout
• Low noise
• Vertical/horizontal offset
• Crystal-to-detector 1 m

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The Blu-ice Control System
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Sample Tab
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Sample Visualization
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Automated Sample Annealing Stop Flow

• Programmed cryo-cooler to stop cold flow
• No icing nitrogen warm stream protects crystal
• Variable annealing time
• Software protected from accidental annealing

Nitrogen Warm Stream
Nitrogen Cold Stream
Myglobin
Annealed for 2 s
Refined Mosaicity 0.31 degrees
Refined Mosaicity 0.15 degrees
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Automated Sample Annealing Stream Block

• Physically blocks the stream close to the sample
  for faster annealing.
• May be controlled through the software or
  manually by pushing a button on the hardware.
• Variable annealing time
• Software protected from accidental annealing

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Simple Robot Control Interface
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Stanford Automated Mounting System
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Sample Storage Cassette
Stores 96 samples mounted on standard Hampton
pins
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Sample Storage Cassette
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How do I transport my cassette?
The beam line dewar holds 3 cassettes or up to
288 samples.
Cassette transfer handle
Ship 2 cassettes inside a Taylor Wharton or MVE
dry shipper
Store 20 cassettes inside a Taylor Wharton HC35
storage device
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How do I put crystals into cassettes?

• Sample Cassette and Hampton pins
• Dewar Canister replaces stock canister in dry
  shipping dewars
• Teflon Ring to support the canister in the
  shipping dewar
• Transfer Handle for handling cold cassettes
• Magnetic Tool to mount pins in cassette to
  test pin size
• Guide Tool to aid mounting pins into cassettes
• Styrofoam Spacer keeps single cassette in place
  when shipping

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How do I get the cassettes and tools?
Manufacturing directions are available online at
smb.slac.stanford.edu/hardware
www.crystalpositioningsystems.com
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The Dispensing Dewar
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The Robot and Gripper Arms
Epson ES553 Robot
Z
U
Vertically Opening Gripper Arms
?1
?2
Cryo-tong Cavity
Fingers to Hold Dumbell Magnet Tool
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Force-Torque Sensor
FORCE-TORQUE SENSOR
FINGERS TO HOLD MAGNET TOOL
CRYO-TONG CAVITY
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Force-Torque Sensor

• Collision Detection
• Automated Calibration
• Status Check
• Probe Samples

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SAM Reliability is Key to Remote Access

• What is a failure?
• Requires Staff Intervention
• Loss of a sample is a very rare failure
• With remote access -- robot failure could lead to
  loss of remaining beam time.
• Enhanced feedback increases reliability
• cryo-tong sensor
• tong drying heater sensor
• laser displacement sensors
• Force sensor

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SAM Reliability Results

• 2005
• - 50 of users used SAM routinely
• - Over 20,000 crystals were screened in 2005
• - 1 failure (intervention) / 400 samples
• 2006
• - SAM was used for over 75 of experiments
• - 50 of our users were running remotely
• JCSG has screened a total of 15,000 crystals
  using SAM and solved over 300 structures.
• In total, approximately 100,000 crystals have
  been screened using the SAM systems at SSRL.

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SAM Reliability Results

• 2005
• - 50 of users used SAM routinely
• - Over 20,000 crystals were screened in 2005
• - 1 failure (intervention) / 400 samples
• 2006
• - SAM was used for over 75 of experiments
• - 50 of our users were running remotely
• JCSG has screened a total of 15,000 crystals
  using SAM and solved over 300 structures.
• In total, approximately 100,000 crystals have
  been screened using the SAM systems at SSRL.

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Pin Problems
EXCESS GLUE OR GREASE
MICROTUBE NOT SECURELY ATTACHED
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Pin Problems
STICKY PINK NAIL POLISH USED INSTEAD OF GLUE
Use epoxy to affix loops in pins Use
permanent marker to mark pins
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Clearing Port Jams
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Easy to Support
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Cross Compatibility
Two types of containers may be used for automated
sample mounting at SSRL The Cassette or the
Uni-Puck
Do not confuse Uni-Pucks with the original ALS
puck. Only Uni-Pucks work with both the SAM and
ALS robots.
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Help General User Community
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The Uni-Puck Project
SSRL, ALS, SBC (APS), CHESS, NSLS, MSC, MAR
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The Uni-Puck Project

• The Uni-Puck is back compatible with the original
  ALS cryo-tools
•  

• Interchangeability of the universal puck base
  and enclosure with the ALS
• puck parts enable rapid transfer of samples
  between these two containers.

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The Uni-Puck with SAM
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The Uni-Puck
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Simple Robot Control Interface
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Simple Robot Control Interface
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Screening Interface
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Crystal Information Excel File
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Automated Crystal Analysis
Diffraction images are scored automatically
during screening Results are displayed in BluIce
and WebIce and saved in excel spreadsheet
Image analysis algorithms used for automated loop
centering The strategy can be imported into the
collect tab
WebIce interfaces to external analysis software
SPOTFINDER (diffraction spot location and image
analysis), LABELIT (autoindexing), MOSFLM (data
integration and strategy), BEST (exposure time),
RADDOSE (absorbed dose calculation)
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Scan Tab
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Automated Energy Selection

• Click on an elemental absorption edge of choice
• Click on Start Scan
• Moves detector to sample
• Uses filters to maximize signal
• Records data across absorption edge using
  appropriate step size
• Runs AutoCHOOCH
• Displays results with selected energies for f,
  f and a calculated remote energy with manual
  override capability
• Click on Update to transfer energies to Collect
  tab

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How to Conduct a Remote Access Experiment
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How Do I Become an SSRL User?
http//smb.slac.stanford.edu/public/forms/becoming
user/

• 1. Submit a Proposal
• Standard General Use Proposals
• Single experiment or Program proposal
• Proposal deadlines are set for April 1, July 1
  and December 1 of each year.
• Applications are reviewed for scientific merit
  and rated on a scale of 1 5.
• Proposals are eligible for beam time for a
  two-year period. 
• http//www-ssrl.slac.stanford.edu/users/user_admi
  n/px_proposal_guide.html
• Rapid Access Proposals
• Normally 5-8 shifts are reserved each
  scheduling period for Rapid Access time.
• Applications are reviewed for scientific merit
  and feasibility for data collection within 1
  month
• The highest ranked proposal will be granted some
  or all of the shifts held in reserve. 
• Other high ranking proposals are given
  consideration when cancellations occur.
•  http//smb.slac.stanford.edu/forms/beamtime/rapid
  _access.html

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Will My Proposal Get Beam Time?
(Demand requested shifts / available shifts)

• - BL9-2 and BL11-1 were in over demand by a
  factor of 2.
• The overall demand (145) could not be met even
  though all five beam lines were
• fully utilized.
• It is anticipated that the availability of
  beam lines 7-1 and 12-2 will add capacity
• to accommodate future demand.

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Will My Proposal Get Beam Time?
As a result of the efficiency of SAM, user
groups often finished early in 2005 and 2006.
Users have begun to compensate for the
screening efficiency by sending more samples or
requesting less beam time per run
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The Australian Synchrotron
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How Do I Become an SSRL User?
http//smb.slac.stanford.edu/public/forms/becoming
user/
2. Become a Participating Research Team Most of
SSRL's beam lines are primarily devoted to
general use access. However, several
institutions have set up Participating Research
Team agreements.  For more information
regarding macromolecular crystallography PRTs,
contact Mike Soltis (soltis_at_slac.stanford.edu). 3
. Collaborate with the SSRL Scientific Staff If
you are interested in establishing a
collaboration with a member of the SSRL staff,
have an unusual experimental set-up, or have
inexperienced group members who need training,
please contact Mike Soltis (soltis_at_slac.stanford.e
du).
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Beam Time Requests

• Spokespersons with active proposals are notified
  via email to submit a request form
• New beam time requests are required 3 times a
  year and are due 2 months in
• advance of each scheduling period
• Beam time request form
• http//smb.slac.stanford.edu/public/forms/beamti
  me/biobtrf_12-05.html
• For remote access check that you want to
  collect data remotely
• Other Paperwork
• A Use Agreement must be completed and turned in
  before your beamtime
• http//www-ssrl.slac.stanford.edu/users/user_admin
  /useagreementmenu.html
• New users are required to sign and submit the
  SSRL Computer Agreement Form http//smb.slac.stan
  ford.edu/public/facilities/computing/Accounts

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Beam Time Preparation

• Read Online Documentation
• User Guide http//smb.slac.stanford.edu/pub
  lic/users_guide/index.shtml
• Blu-ice Manual http//smb.slac.stanford.edu
  /facilities/software/blu-ice/
• 2. Acquire a Cassette Loading Kit (contact Lisa
  Dunn)
• 3. Acquire a Dry Shipping Dewar
• Dewars that fit cassettes MVE model SC 4/2V
  (recommended),
• Taylor Wharton CP100 or CX100, or International
  Cryogenics IC-7VS
• Dont procrastinate Do not wait until the night
  before your shipping deadline to load all your
  samples into your cassette.
• Cassettes should arrive at least one day in
  advance of your beam time. Shipments are not
  delivered to SSRL on holidays or weekends.

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5. Keep track of your crystals as you load your
cassette. Use the SSRL template excel file.
Upload this information to the SSRL screening
database. https//smb.slac.stanford.edu/crysta
ls/
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• 6. Carefully Read and Follow the dewar shipping
  directions.
• Remote Users are required to fill-out and
  follow the procedures described on our online
  dewar shipping form
• http//smb.slac.stanford.edu/public/forms/sh
  ipping/DewarToSSRL.html
• After filling out the online form you
  should save the .pdf file that is created.
• This file contains shipping labels and a
  return shipping form.
• 1. Attach a shipping label to each dewar.
• 2. Include a return shipping form inside
  the dewar.
• If the online shipping form is used
• You will be notified via email when your dewar
  arrives to SSRL
• Your dewar will be delivered to the beam line.
• If requested, your dewar will be filled with
  liquid nitrogen

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7. Use the Support Staff Schedule to lookup your
support staff scientist. This is your contact
person. http//smb.slac.stanford.edu/schedule/
sch_staff.cgi 8. Email your user-support staff
person to ensure they have your phone number and
email address.
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• 9. Install the NX client software on your data
  collection computer
• 10. Contact your support scientist to arrange to
  test your NX connection before you beamtime.

www.nomachine.com
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11. A dataset is available to practice using
strategy and data processing software located in
the /data/mb_example directory.
http//smb.slac.stanford.edu/facilities/software/

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During Your Beam Time
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During Your Beam Time
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During Your Beam Time
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During Your Beam Time
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During Your Beam Time
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Data Backup
Remote network transfer - scp/sftp DVD Submit
request using a web interface to generate DVDs
for mail delivery. http//smb.slac.stanford.edu/
facilities/computing/dvd-interface.html
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After Your Beam Time

• 1. Complete and End of Run Summary Form
• http//www-ssrl.slac.stanford.edu/users/user_
  admin/form_ers.html
• 2. All publications related to work fully or
  partially undertaken at
• SSRL should contain the following
  acknowledgement
• "Portions of this research were carried out
  at the Stanford Synchrotron Radiation Laboratory,
  a national user facility operated by Stanford
  University on behalf of the U.S. Department of
  Energy, Office of Basic Energy Sciences. The SSRL
  Structural Molecular Biology Program is supported
  by the Department of Energy, Office of Biological
  and Environmental Research, and by the National
  Institutes of Health, National Center for
  Research Resources, Biomedical Technology
  Program, and the National Institute of General
  Medical Sciences."
• 3. Include references to software and hardware
  used during your
• experiment.
• http//smb.slac.stanford.edu/public/users_gui
  de/manual/Referencing_SSRL.html
• 4. It is very important that you tell us about
  publications relevant to work conducted at
  SSRL http//smb.slac.stanford.edu/forms/reporting
  /form_publication.shtml

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Thanks for your attention