Publishing MX data

Owned by MX Cluster (Unlicensed)
Last updated: Oct 16, 2023 by AS MX Wiki
3 min read

Vital information for publishing

There are four things you must include when publishing data from MX:

  • Reference the beamline paper. Please do this in the main paper, not in the supplementary information.

  • Acknowledge the Synchrotron. The references usually go in this acknowledgement, not in the supplementary information.

    • MX1: “This research was undertaken in part using the MX1 beamline at the Australian Synchrotron, part of ANSTO.”

    • MX2: "This research was undertaken in part using the MX2 beamline at the Australian Synchrotron, part of ANSTO, and made use of the Australian Cancer Research Foundation (ACRF) detector"

  • Reference the software used for data collection and processing

  • Include the correct information in your cif/mmcif. See below for CX or PX relevant information.

“Why do I need to do this?”

In part, because it’s just good practice to acknowledge the resources you’ve used in your research. The other reason is that it helps us at MX & ANSTO analyse what sort of science is being done on the beamlines. This can help us apply for funding for improvements to the beamlines. When we are asked “how many chemical crystal structures were solved using MX1 in 2020?” we have a limited number of ways of tracking down this information. We can search for publications citing the MX papers, and we can search databases for identifying fields in cifs and mmcifs. If your work doesn’t have these identifying features, we can’t find it and point to it as a good example of how the beamlines are being used.

By including all the correct acknowledgements when publishing, you give us the tools we need to keep expanding and improving the beamlines.

 

Protein Crystallography

Depositing Data

Publication of structural data usually requires the deposition of that data to the Worldwide Protein Data Bank. This process involves submitting validated mmcif files and filling in experimental and collection details.

The wwPDB deposition webpage can be found here.

Generating Table 1

Crystallographic data are typically presented in papers in the form of a ‘Table 1’ table. The exact format of this table and the information that should be included will vary journal to journal. You should find examples of Table 1 tables from the journal you plan on submitting your manuscript to, and model your table accordingly.

Table 1 can be generated using Phenix’s “Generate Table 1 for journal” tool, found under the PDB Deposition toolbar. You will need to provide unmerged reflections (eg. an HKL file output by XDS, or the initial unmerged mtz file from imosflm) and your final pdb and working mtz files.

Chemical Crystallography

NEW!! CX-ASAP

CX-ASAP automatically runs xprep and shelxt and places the results in the folder labelled “CX-ASAP_Brute” in your dataset folder. If you use these files, please reference CX-ASAP (DOI: 10.1107/S1600576723000298)

Cif file entries (aka cif_od)

The cif file entries which are specific to the synchrotron and your data collection can be found in a cif file which is automatically generated for each dataset you collect., called autoprocess.cif. See https://asuserwiki.atlassian.net/wiki/spaces/UO/pages/409993222 page for more information.

Software references

In addition to referencing the software used for data collection and processing, you must reference the software and interfaces used to solve and refine your structure. Below is a list of the common software used in structure solution and refinement, generating graphics and further data processing and analysis. Keep in mind that this is not comprehensive, and you should reference all software you use.

Other crystallographic software references are available here.

A summary of SHELX programs and their associated references can be found in this publication.

Beamline techniques

If you use Diamond Anvil cells on MX1, please reference this paper: High-pressure single-crystal diffraction at the Australian Synchrotron