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Beamline Connectivity


NX NoMachine; X2Go:

  • NX Nomachine; client version
    • preferred software, as staff able to "shadow" your login session, and thus offer more extensive User Support
    • availablew for PCs, Macs, or Linux
  • X2Go; an alternative to NX Nomachine clients, above:
    • SER-CAT staff unable to "shadow" your login session (i.e. staff unable to help and/or advise via this route)
    • available for PCs, Macs, or Linux

SERGUI - an overview


Open a new terminal window, and type:

Data Collection Protocols


Data collection directories:

A User may choose to use one of several pre-defined protocols for their data collection strategy. Using one of these can make subsequent data collection more organized, and help prevent accidental over-writing of previously collected images.

If desired, a User may choose instead to import and load an excel spreadsheet containing sample information, then use this information as part of the hierarchical naming scheme for data collection and processing. This is most easily accomplished by creating an excel spreadsheet, which has been tab delimited, then saved this file as filename.csv.

Should the User choose to not load a previously prepared spreadsheet or pre-defined protocol, the default hierarchical naming convention will be: puck name, pin number, single/run number (eg. Pn8p3s1 for "puck number" 8, "pin" 3, "single" image number 1).

Robot Automounter


The Both beamline 22-ID and 22-BM are equipped with a robotic sample mounter:

  • 22-ID:
    • up to 30 Uni-pucks
      • 20 pucks with all pin positions accessible
      • 10 pucks with 13 out of 16 pin positions available (unable to access positions 6, 7 and 16)
  • 22-BM
    • up to 6 Uni-pucks
      • all pin positions accessible

Beamline Tools


Accessed by the robot are certain beamline tools:

  • Phosphor:
    • on 22-ID, YAG crystal is preferrable for aligning your beam (mounted on same stage as crystal alignment slides); in principal, phosphor could also work, and one is available
    • on 22-BM, phosphor is preferred way to align your beam (YAG crystal mount separated from crystal alignment slides and goniometer)
    • on either 22-ID or 22-BM, aligned phosphor is first step towards verifying that goniometer height coincides with cross-hairs (and is aligned with x-ray beam)
  • Alignment pin: used to ascertain "point and click", "goniometer rotation axis"
    • a sharp-pointed pin, available for "point and click" verification
    • successful alignment of tip at all goniometer orientations verifies goniometer rotation axis coincides with cross-hairs (used for "point and click", as well as alignment of x-ray beam position)
  • Trypsin crystal (standard; primitive orthorhombic, space group P212121)
    • though this crystal may appear icy towards the end of the run, it will continue to diffract beautifully and provides an in-house standard for beamline verification

Beamline Optimization


Before starting a data collection, it is wise to check the optimization of your beamline:

  • 22-ID:
    1. tune the beamline
    2. table alignment
    3. vertical pin-hole alignment
    4. horizontal pin-hole alignment
  • 22-BM:
    1. tune the beamline
    2. vertical "pin-hole" (guard-slit scan)
    3. horizontal "pin-hole" (guard-slit scan)

Changing Energies


SER-CAT beamlines are usually set to 1.00 Å wavelength for the beginning of your time-slot, but both MAD and SAD experiments often require changes of this parameter. The method for accomplishing a wavelength change is slightly different on 22-ID and 22-BM:

  • 22-ID:
    • one may enter desired energy in eV (note: NOT keV!) - OR...
    • one may enter desired energy in wavelength (lambda, measured in Å)
    • note that the undulator gap energy will be slightly higher in eV than the desired energy; this is normal, and is a function of APS calibration considerations
  • 22-BM:
    • one may enter desired energy in eV (note: NOT keV!) - OR...
    • one may enter desired energy in wavelength (lambda, measured in Å)
    • there is no undulator for a bending magnet beamline - so no gap energy, either

Collecting Data


Set-up occurs in a series of steps:

  • Mounting and aligning crystals:
    • SER-CAT staff member loading pucks into beamline dewar(s)
    • User choice of puck/pin from available pucks
    • Auto-loop alignmenmt of sample
    • 2-point crystal alignment; point and click
    • Manual alignment; point and click
  • Fluorescence scans
    • Mount a poor-quality crystal from your project
    • Take a "single" diffraction image, to make sure crystal is centered in x-ray beam
    • Run a scan with low transmission to avoid detector saturation
    • Click on "Analyze", to analyze the scan
  • Data collection setup; single pass
    • Collect single images in different orientations under the "Collect Single" tab
    • Set up and upload data collection parameters under the "Collect Strategy" tab
    • Start data collection under "Collect Runs" tab
  • Data collection setup; MAD
    • Collect single images in different orientations under "Collect Single" tab
    • Set up data collection parameters under the "Collect Strategy" tab
    • Enter/check the peak, edge and remote energies from the fluorescence scan
    • Upload the parameters and collect data sets under "Collect Runs" tab
  • Rastering
    • Center the loop and click on Automation -> Sample Rastering on "sergui"
    • Click "Yes" to the pop-up window, requesting: "Do you want to open the help PDF for rastering?"
    • Follow the instructions in the PDF for sample rastering
  • Helical data collections
    • Center the crystal and click on Automation -> Helical Data Collection on "sergui"
    • Click "Yes" to the pop-up window, requesting: "Do you want to open the help PDF for helical data collection?"
    • Follow instructions in the PDF for helical data collection
  • The most recent and reliable direct beam information is obtained by typing:
    • ssbeamxy aps22id (or: ssbeamxy aps22bm); this will return a list of the following:
      • Definitions of various different detectors
      • Directbeam coordinates, as required for various processing packages
      • Command-line User Input commands for quick and automatic data processing when using SER-CAT computer systems
      • Also, the relevant direct beam information for your data collections (along with a great deal of other useful information) will be automatically be saved for you in the following location(s):
        • /data/ID_name_institution.raw/beamcenter_22ID.dat (or analogous gzipped file)
        • /data/BM_name_institution.raw/beamcenter_22BM.dat (or analogous gzipped file)

Data Processing


A number of automatic evaluation processes will be occurring:

  • Albert's automation, which will automatically perform the following, as long as the data collection is not aborted part way through data collection:
    • Command-line User input commands for quick and automatic data processing when using SER-CAT computer systems
    • The automated data processing files and results will be under the "zz*.." sub-directories
    • A summary of automated data processing results can be found under Processing -> Auto Process Log on "sergui"
  • Use a different computer for processing your data; doing this will help avoid impacting your on-going data collections
  • Remember that SER-CAT is presently using the following two types of detectors:
    • 22-ID: Eiger X16M (Dectris)
    • 22-BM: MX300-HS (Rayonix)
  • Obtaining directbeam coordinates, required for various processing packages, is best found by checking the information automatically stored in the file located at (depending upon beamline):
    • /data/ID_name_institution.raw/beamcenter_22ID.dat
    • /data/BM_name_institution.raw/beamcenter_22BM.dat

Data Backups


The most recent and reliable site file information is obtained by typing:

  • Globus GridFTP:
    • Secure, robust data transfer using FTP protocol
    • Dedicated SER-CAT GridFTP onsite server; remote user data transfer will not drag down the local network and file access performance
    • User can start data transfer from SER-CAT archive system to their home institutions archive by using Globus Connect Personal protocol - anywhere, anytime
    • Interrupted data transfer can be resumed anytime
  • Sending a portable Linux hard drive (EXT3 formatted):
    • Windows and Mac formats (eg. FAT32, exFAT, NTFS, APFS, and HFS+) are NOT supported by SER-CAT
    • Make sure there is sufficient room on the hard drive for your anticipated backup requirements; be optimistic, and guesstimate high for your requirements
    • If the drive is brand new, SER-CAT staff can format to EXT3 format for you, before backing up your data to the drive

Frequently Asked Questions (FAQ)


A certain number of questions tend to arise frequently; you might be able to find your answer below:

  • Useful Reminders are included in this pdf, including answers to:
    • I started a data collection and I see blank images with no diffraction
    • APS stored beam was lost and it just came back; what should I do?
    • I can not see my sample
    • I am not able to open the "sergui" program
    • I collected some data sets and I would like to quickly look at auto-processing results
    • Where can I find the beam center values?
    • I sent too many samples and have lost track of which crystals I have already mounted; do you have that information somewhere?
    • My NX-client fails to connect to the SER-CAT computers

Websites of Interest


Links in this section are provided as a convenience for Users; some contain information related to structural biology, others are more physics and beamline related.

  • Crystallographic Associations:
    • ACA (American Crystallographic Association)
    • IUCr (International Union of Crystallography)
    • ...and many more... (IUCr listing of National and Regional Societies)
  • Synchrotron Facilities:
    • USA
      • Download sgxpro.tar (a link) and save it to where you want to put the package
      • From there type command: tar xvf sgxpro.tar; ./sgxpro_install
      • CHESS (Cornell High Energy Synchrotron Source; Ithaca, New York)
      • NSLS II (National Synchrotron Light Source II; Brookhaven, New York)
      • SSRL (Stanford Synchrotron Radiation Lightsource; Stanford, California)
    • Everywhere (!)
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