efficiency with a commensurate increase in the volume of novel, and increasingly
more challenging, protein structures that have been determined.
With the rapid development of sample preparation and data collection infrastructure, there has been a strong drive to manage the overwhelmingly large volumes of
data that can be generated at each stage of the process: from initial sample production
through to the finally realised crystal structure. To this end, many synchrotrons have
developed a laboratory information system (LIMS). The LIMS system at Diamond,
more widely known as ISPyB, provides a portal for users to track each stage of their
experiment; detailed sample information can be added for each sample ahead of
beamtime, along with the location of each sample within the shipping container.
ISPyB can be used to generate the appropriate labels for the shipping containers to
allow them to be couriered, and tracked, to the synchrotron. At the commencement
of beamtime, ISPyB is updated with the specific location of each sample within the
beamline’s robotic sample changer. The location and all of the accompanying
sample information can then be moved to the beamline’s data collection, GDA,
software from which each sample can be called and mounted for data collection.
Usually data collection is carried out by the user accessing the beamline via remote
login via their home institution. All of the raw and processed diffraction data is then
linked to each sample along with all of the accompanying metadata, including the
beamline parameters and images (snapshots) of the crystal from the beamline’s
sample viewing optics.
There has been a large shift for macromolecular crystallography to make LIMS,
such as ISPyB, the core of the data collection, and data curation, process and to make
the database itself the principal means of user interaction for all steps. For small
molecule crystallography, progress in this area has been somewhat slower as there
are few dedicated beamlines that exclusively support this technique and only a
subset of these have any degree of robotic sample exchange. Beamline I19 at
DLS, however, has facilities that are reminiscent of those on MX beamlines,
including large-format pixel array photon counting detectors and a robotic sample
changer, and is fully incorporated into the DLS GDA infrastructure. As a consequence, it is more fully compliant with the requirements for integration with ISPyB.
Following the upgrade to the high-throughput diffractometer and robotic sample
changer in experiments hutch 1 (EH1) of beamline I19 [49], there has been the
adaptation of ISPyB to enable the recording of metadata specific to small molecule
crystallography.
For MX, after initial data processing, the unit cell can be compared with similar
cells for the user’s current visit and previous visits, and the cell can also be searched
for within the Protein Data Bank (PDB). For small molecule crystallography, a cellmatching search for similar unit cells in the user’s current and previous visits can be
undertaken, but, as yet, any search in the Cambridge Structural Database (CSD)
needs to be undertaken outside the environment of SynchWeb with the CSD
application ConQuest. It can be envisaged, however, that a suitable interface could
be developed to pass cell information from SynchWeb to ConQuest or to provide a
relatively seamless link between both applications.
Leading Edge Chemical Crystallography Service Provision and Its Impact on. . .
89
more challenging, protein structures that have been determined.
With the rapid development of sample preparation and data collection infrastructure, there has been a strong drive to manage the overwhelmingly large volumes of
data that can be generated at each stage of the process: from initial sample production
through to the finally realised crystal structure. To this end, many synchrotrons have
developed a laboratory information system (LIMS). The LIMS system at Diamond,
more widely known as ISPyB, provides a portal for users to track each stage of their
experiment; detailed sample information can be added for each sample ahead of
beamtime, along with the location of each sample within the shipping container.
ISPyB can be used to generate the appropriate labels for the shipping containers to
allow them to be couriered, and tracked, to the synchrotron. At the commencement
of beamtime, ISPyB is updated with the specific location of each sample within the
beamline’s robotic sample changer. The location and all of the accompanying
sample information can then be moved to the beamline’s data collection, GDA,
software from which each sample can be called and mounted for data collection.
Usually data collection is carried out by the user accessing the beamline via remote
login via their home institution. All of the raw and processed diffraction data is then
linked to each sample along with all of the accompanying metadata, including the
beamline parameters and images (snapshots) of the crystal from the beamline’s
sample viewing optics.
There has been a large shift for macromolecular crystallography to make LIMS,
such as ISPyB, the core of the data collection, and data curation, process and to make
the database itself the principal means of user interaction for all steps. For small
molecule crystallography, progress in this area has been somewhat slower as there
are few dedicated beamlines that exclusively support this technique and only a
subset of these have any degree of robotic sample exchange. Beamline I19 at
DLS, however, has facilities that are reminiscent of those on MX beamlines,
including large-format pixel array photon counting detectors and a robotic sample
changer, and is fully incorporated into the DLS GDA infrastructure. As a consequence, it is more fully compliant with the requirements for integration with ISPyB.
Following the upgrade to the high-throughput diffractometer and robotic sample
changer in experiments hutch 1 (EH1) of beamline I19 [49], there has been the
adaptation of ISPyB to enable the recording of metadata specific to small molecule
crystallography.
For MX, after initial data processing, the unit cell can be compared with similar
cells for the user’s current visit and previous visits, and the cell can also be searched
for within the Protein Data Bank (PDB). For small molecule crystallography, a cellmatching search for similar unit cells in the user’s current and previous visits can be
undertaken, but, as yet, any search in the Cambridge Structural Database (CSD)
needs to be undertaken outside the environment of SynchWeb with the CSD
application ConQuest. It can be envisaged, however, that a suitable interface could
be developed to pass cell information from SynchWeb to ConQuest or to provide a
relatively seamless link between both applications.
Leading Edge Chemical Crystallography Service Provision and Its Impact on. . .
89