PDBe (EBI) and STFC are developing a web service as part of the BioMedBridges project (http://www.biomedbridges.eu/workpackages/wp9) that will enable the EMDB and PDB archives to be searched on the basis of 3D volumetric shape matching, rather than solely on the basis of metadata and/or coordinate model.

For example:
- users will be able to upload a 50S ribosome map and retrieve aligned maps of other ribosomes from the archives
- when new entries are deposited, the service will automatically fit and segment existing entries that share common components, e.g. a newly deposited ribosomal protein will be fitted into ribosomal maps in the PDB/EMDB. The resulting segmentations will be made publicly available.

In due course, the service may be extended to other volumetric data, such as from SAXS or soft X-ray tomography.

In February-March 2013, we asked the community for input on shape/volume matching. The questions covered protocols followed, usage issues, as well as specific software. A report on the findings can be viewed at http://www.biomedbridges.eu/biomedbridges-wp9-shape-matching-survey

We now wish to consult the community regarding volume segmentation, which in many cases will be a necessary step before volume matching. We would like to know what tools you use and in which context you use these tools. Your answers will help inform our development, and ensure the service meets the needs of the community. While the proposed service is most relevant to structural biologists, segmentation is a widely used technique, and input from other communities would be very useful.

Many Thanks,
Ingvar Lagerstedt & Ardan Patwardhan, PDBe (EBI) and Agnel Praveen Joseph & Martyn Winn, STFC

* 1. Do you currently perform 3D volume segmentation?

* 2. What types of data do you (or would you like to) segment? (Please select all that apply.)

* 3. What type of segments do you look for? (Please select all that apply.)

* 4. What type of segmentation do you do? (Please select all that apply.)

* 5. What software are you using for segmentation? (Please select all that you use.)

* 6. Do you need to train the software to recognise appropriate segments?

* 7. If you use more than one software package, do you follow a protocol for choosing which software to use for a given case?

* 8. How do you typically access the software? (Please select all that apply.)

* 9. If your volume data has symmetry elements, such as in viruses, chaperones, helices etc., is this taken into account?

* 10. How do you evaluate the results? (Please select all that apply.)

* 11. How do you add annotations to the segmentations?

* 12. Please provide details of any options/features that are particularly useful in the packages you use and worth highlighting

* 13. What is your role?

Thank you for taking the survey!

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