Dear Laurent, sorry for getting into this discussion a bit late, but I was traveling. Many good points have been raised in response to your question. I'd like to summarize and add to them.
1. Your beamline scientist WILL know how to process the data, and if the software she recommends is not what you're familiar with, she will also be able to help you with your favorite software. This should always be your first port of call. 2. HDF5 in itself doesn't pose problems to XDS. If the HDF read library Neggia that was mentioned in a few of the responses doesn't help XDS read HDF5 files, let me and Kay Diederichs know. We'll try to figure out the problem. 3. XDS pipelines (autoProc, xdsme, xdsgui, xds-app, etc) should be able to process HDF5 data as long as they know where Neggia is located. 4. HDF5 files written by the detector should all look the same (files written when the detector was introduced looked slightly different). Many beamlines are now streaming the data off the detector and write the files themselves. Here, considerable variety in the metadata is possible. We are working on a validator for HDF5 metadata, but that's still work in progress. 5. Besides XDS, DIALS and HKL-2000 should process HDF5 files without complaints. 6. Conversion of HDF5 files into CBF is still required for processing with iMosflm, but that's likely to change before too long. 7. Our tool H5ToXds is technically not a converter but an extractor. It writes the images in headerless CBF, which is not a standard. H5ToXds was written with the singular purpose of helping XDS process HDF5 data by presenting individual images as temporary CBFs upon request. Since the introduction of the plugin mechanism and Neggia, H5ToXds is obsolete. If you do need to create CBFs, eiger2cbf or hdf2mini-cbf should be used. They write miniCBF headers. Best is to work with HDF5, though. 8. The source code for eiger2cbf (https://github.com/biochem-fan/eiger2cbf) doesn't just contain a CBF converter but also a plugin for XDS. This plugin does the same thing as Neggia but works even better under extreme load (data from NSLS-II). I'm happy to answer any questions that might remain. Thanks to everyone for answering. All best. Andreas On Thu, May 31, 2018 at 8:58 AM, maveyrau <laurent.maveyr...@ipbs.fr> wrote: > Hi CCP4ers > > we recently collected many datasets on dectris detectors producing hd5 > files. I would like to use some auto processing tools to process them > (xdsapp, xdsme…). As far as I can say, xdsapp or xdsme cannot process hd5 > natively. I tried to convert them to cbf format (eiger2cbf, > hdf2mini-cbf,...), but then it seams that the header of the caf files are > lacking some required informations… > > Any idea how to convert hd5 files to complete caf files ? Are there any > plans for xdsapp to be able to work on hd5 files ? > > thanks for your help > > Laurent > ---------------------------------------------------------- > Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr > P I C T --- Plateforme Intégrée de Criblage de Toulouse > Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 > Département Biologie Structurale et Biophysique > http://cribligand.ipbs.fr http://www.ipbs.fr > 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE > Tél: +33 (0)561 175 435 Mob.: +33 (0)646 042 111 > ---------------------------------------------------------- > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- <https://www.dectris.com> Andreas Förster, Ph.D. Application Scientist Crystallography, Scientific Sales Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: andreas.foers...@dectris.com DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | www.dectris.com [image: LinkedIn] <https://www.linkedin.com/company/5067919> [image: facebook] <https://www.facebook.com/pages/Dectris-Ltd/623855944369304> <https://twitter.com/DECTRIS_News> Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
