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RE: Draft COMCIFS 2016 report
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
- Subject: RE: Draft COMCIFS 2016 report
- From: "Brown, David" <idbrown@mcmaster.ca>
- Date: Thu, 23 Mar 2017 14:21:05 +0000
- Accept-Language: en-CA, en-US
- In-Reply-To: <CAM+dB2egpepgr8DpVBr6X9cx16B_UYybmWaQ82dMcBNi7+96cg@mail.gmail.com>
- References: <CAM+dB2egpepgr8DpVBr6X9cx16B_UYybmWaQ82dMcBNi7+96cg@mail.gmail.com>
James,
I would suggest adding the names of the voting members of COMCIFS to the first paragraph along with a brief description of the way COMCIFS operates. This will give the Executive Committee (and other readers) a bit of context. It is also useful to have an archival list of the voting membership as this information can get lost in our rather informal mode of operation. Keep up the good work. David I. David Brown
Professor Emeritus Department of Physics and Astronomy McMaster University Hamilton, Ontario, Canada From: comcifs [comcifs-bounces@iucr.org] on behalf of James Hester [jamesrhester@gmail.com]
Sent: March 22, 2017 21:19 To: Discussion list of the IUCr Committee for the Maintenance of the CIF Standard (COMCIFS) Subject: Draft COMCIFS 2016 report Dear COMCIFS,
Please see below a draft report for the preceding year for submission to the IUCr executive. Please let me know as soon as possible of any errors or omissions.COMCIFS report 2016 =================== COMCIFS is tasked with maintaining and developing the Crystallographic Information Framework (CIF) on behalf of the IUCr. New dictionaries A dictionary describing magnetic structures (magCIF) was produced by the Commission on Magnetic Structures with technical advice from COMCIFS members. It has been approved by COMCIFS and has seen rapid adoption in software dealing with magnetic structures. Updating legacy dictionaries At the 2014 Montreal meeting, COMCIFS resolved that all dictionaries written in the legacy DDL1 language would be converted to the new DDLm language. A DDLm version of the core CIF dictionary, upon which most other dictionaries depend, was approved by COMCIFS towards the end of 2016. Draft DDLm versions of the remaining dictionaries are being sent out to the original authors for checking. As part of this process, authors are able to provide any updates and new definitions, and will be invited to contribute or update chapters for the second edition of International Tables Volume G. Macromolecular standards The wwPDB continued to promote CIF usage in the macromolecular community, with sponsorship of SASCIF expansion efforts [1] and hybrid methods dictionary extensions [2]. The new wwPDB OneDep Deposition & Annotation system [3] (deposit.wwpdb.org) released with added support for NMR and 3DEM Structures. The OneDep system is built on a PDBx/mmCIF data infrastructure representing all of these experimental methods [4]. The X-ray refinement applications CCP4/REFMAC and Phenix.Refine both support the production of PDBx/mmCIF data files ready for deposition. Current dictionaries used by this system are made available on the PDBx/mmCIF resources site mmcif.wwpdb.org. Interaction with other data management initiatives For the past five years, we have worked to achieve interoperability between imgCIF/CBF and NeXus/HDF5 NXmx in describing metadata for macromolecular crystallography diffraction images. This effort has contributed to successful handling of diffraction images from XFEL detectors and Dectris Eiger detectors in both CBF and HDF5 formats [5][6][7][8]. Starting in 2016 there have now been four High Data -Rate Macromolecular Crystallography (HDRMX) meetings (see http://www.medsbio.org/hdrmx/). At the most recent HDRMX meeting, (March 2017) it was agreed to begin mapping both the mmcif and corecif dictionaries into NeXus, so that complete descriptions of the samples studied can be included with diffraction image metadata in the earliest stages of crystallographic studies. This will facilitate both publication and archiving. ====== [1] Extension of the sasCIF format and its applications for data processing and deposition Kachala, M., Westbrook, J., & Svergun, D. (2016). Journal of Applied Crystallography, 49(Pt 1), 302–310. [2] https://github.com/ihmwg/IHM-dictionary/blob/master/dictionary_documentation/documentation.md [3] OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield9, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen, Luigi Di Costanzo, Dimitris Dimitropoulos10, Guanghua Gao, Sutapa Ghosh, Swanand Gore, Vladimir Guranovic, Pieter M.S. Hendrickx, Brian P. Hudson, Reiko Igarashi, Yasuyo Ikegawa, Naohiro Kobayashi, Catherine L. Lawson, Yuhe Liang, Steve Mading, Lora Mak, M. Saqib Mir, Abhik Mukhopadhyay, Ardan Patwardhan, Irina Persikova, Luana Rinaldi, Eduardo Sanz-Garcia, Monica R. Sekharan, Chenghua Shao, G. Jawahar Swaminathan11, Lihua Tan, Eldon L. Ulrich, Glen van Ginkel, Reiko Yamashita, Huanwang Yang, Marina A. Zhuravleva, Martha Quesada, Gerard J. Kleywegt, Helen M. Berman, John L. Markley, Haruki Nakamura, Sameer Velankar, Stephen K. Burley (2017) Structure , Volume 25 , Issue 3 , 536 - 545 [4] NMR Exchange Format: a unified and open standard for representation of NMR restraint data Aleksandras Gutmanas, Paul D Adams, Benjamin Bardiaux, Helen M Berman, David A Case, Rasmus H Fogh, Peter Güntert, Pieter M S Hendrickx, Torsten Herrmann, Gerard J Kleywegt, Naohiro Kobayashi, Oliver F Lange, John L Markley, Gaetano T Montelione, Michael Nilges, Timothy J Ragan, Charles D Schwieters, Roberto Tejero, Eldon L Ulrich, Sameer Velankar, Wim F Vranken, Jonathan R Wedell, John Westbrook, David S Wishart & Geerten W Vuister,(2015) Nature Structural & Molecular Biology 22, 433–434 [5] Brewster, Aaron S., Johan Hattne, James M. Parkhurst, David G. Waterman, Herbert J. Bernstein, Graeme Winter, and N. K. Sauter. "XFEL Detectors and ImageCIF." Computational Crystallography Newsletter 5 (2014): 19-24. [6] Förster, Andreas, Stefan Brandstetter, Marcus Müller, and Clemens Schulze-Briese. "EIGER detectors in biological crystallography." https://www.dectris.com/tl_files/root/applications/macromolecular_crystallography/application/White_Paper_EIGER_May2016.pdf [7] Bernstein, Herbert J., Babak Andi, Kaden Badalian, Lonny E. Berman, Dileep K. Bhogadi, Shirish Chodankar, Jonathan DiFabio, Martin R. Fuchs, Jean Jakoncic, Edwin O. Lazo, Sean McSweeney, Lisa Miller, Stuart Myers, Dieter K. Schneider, Bruno Seiva Martins, Wuxian Shi, John Skinner, Hugo Slepicka, Alexei Soares, Vivian Stojanoff, Robert M. Sweet, Ryan Tappero, and Lin Yang. "Computing infrastructure, software optimization, and real time analysis for high data-rate MX." In Scientific Data Summit (NYSDS), 2016 New York, pp. 1-4. IEEE, 2016. [8] Hester, James. "A Robust, Format-Agnostic Scientific Data Transfer Framework." Data Science Journal 15 (2016) |
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