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Main Content

Macromolecular Crystallography
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In This Section

Sub Navigation
  • VMXi Manual
    • Prepare for VMXi Beamtime
    • Sample Holders
    • ISPyB/Synchweb
      • Select a Proposal
      • Add Lab Contact
      • Create a Shipment
      • Registering Samples
      • Data Collection
      • Data Management
        • Toolbar in ISPyB
        • Experiment Type Views
        • Sample View
        • Beamline Parameters
        • Viewing Diffraction Images
        • Photos of Crystals
        • Per Image Analysis Plot
        • Grid Scans
        • Auto Processing Results
        • Phenix xtriage results
        • Data Quality Plots
        • Downstream Processing Results
        • AlphaFold: Downstream Processing
        • Logs and Files
        • Permalinks
    • Data Analysis
    • Data Backup
  • Acknowledgement and References
  • Beamline Schematic
  • Staff
  • Specification
  • VMXi Photo Gallery
  • Science Highlights and News
  • Publications
  • FAQ

Instruments by Science Group

Macromolecular
Crystallography
Soft Condensed
Matter
Imaging and
Microscopy
Biological
Cryo-Imaging
Magnetic
Materials
Structures and
Surfaces
Crystallography
Spectroscopy

VMXi Contact

Principal Beamline Scientist:
Mike Hough
Tel: +44 (0) 1235 394097
E-mail: [email protected]

More

Science Group Leader

Dave Hall

Email: [email protected]
Tel: +44 (0) 1235 778926

  1. Instruments
  2. MX
  3. VMXi
  4. VMXi Manual
  5. ISPyB/Synchweb
  6. Data Management
  7. Toolbar in ISPyB

Toolbar in ISPyB

At the top of the main data view in ISPyB there are short-cut buttons to various useful functions:
toolbar

VMXi Relevant

  • Summary
  • Autoprocessing
  • Users
  • Reprocessing

Not used on VMXi:

  • Assign Containers 
  • Dewars
  • Sample Changer
  • Visit Stats
  • Beamline status

Summary

The summary link summises Data collections in a tabular format. If there are a large number of datasets for a VMXi plate, this can be quite slow to load.

data collection summary

The table contains all data collections, each summarised with:

  • Data collection prefix: used in file naming
  • Sample
  • Date and time collected
  • Number of images
  • Degrees of oscillation
  • Seconds exposed per frame
  • Relative transmission percentage
  • Number of autoprocessing pipelines run (#AP) [ Not accurate]
  • Spacegorup (Most common found, and by what pipeline)
  • Unit cell
  • Resolution limits, and inner and outer shellls
    • With the Rmeas and Completeness
  • A download link to mtz file [Currently not working]

Note that the data can be filtered using the search box, but the sorting (clicking the top of a column) is currently not working. 

Autoprocessing

The autoprocessing summary shows which autoprocessing pieplines have run:

autoprocessing summary

The cog allows reprocessing for the dataset. The arrow redirects to the dataset.

Users

Hover over the icon to see a list of people involved in the visit. 

Users are added to proposals by the BAG PI, in UAS. You need to be added to a proposal to be able to access data from the visit, as well as those Users involved in data collection.

Reprocessing

A reprocessing panel appears to re-submit automatic processing pipelines with different parameters. See full details in reprocessing data.

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