Re: [ccp4bb] processing hd5 files from Dectris detector
Hi All, I doubt it is on MASSIF-1, we still have a Pilatus3 2M, but I guess more on Massif-3 if collected at ESRF. People very often confuse between the two. Massif-1 is the fully automatic beamline and Massif-3 is the microfocus. Cheers. D On 01/06/2018 11:03, Harry Powell wrote: Hi Laurent has contacted me off-board about this and sent me an example of a CBF file extracted from the HDF5. As far as I can see, there is no problem with the CBF file created by eiger2cbf - it can be processed correctly by iMosflm, and the miniCBF header is not missing any of the information that Mosflm requires. From this, I think that there's an issue with XDSAPP - so probably something for Manfred to have a look at! In answer to Kay's questions - (1) Massif-1 (2) That would be my first port of call... (3) not tried yet... (4) the exact error messages start with what Laurent gave originally, i.e. - Some important experimental parameters are missing from the images header which is not so useful, but there is an additional traceback - Some important experimental parameters are missing from the images header Traceback (most recent call last): File "/mnt/maredsous/programs/bin/xdsit.py", line 4018, in manual_process() File "/mnt/maredsous/programs/bin/xdsit.py", line 3897, in manual_process manual_index() File "/mnt/maredsous/programs/bin/xdsit.py", line 3885, in manual_index print(params['detector']) KeyError: ‘detector' Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 1 Jun 2018, at 07:21, Kay Diederichs wrote: Hi Laurent, this prompte a couple of questions - 1. where did you collect the data? 2. can this not be answered by the beamline staff? After all they should know their detector, and procedures for use of its data. 3. what are the exact error messages when using the neggia plugin? I guess Dectris would care if their plugin cannot read "their" data. 4. what are the exact error messages / missing items when using eiger2cbf / hdf2cbf-mini? best, Kay On Thu, 31 May 2018 14:58:52 +0200, maveyrau mailto: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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] CALL for PROPOSAL on ESRF BIO-SAXS BEAMLINE ID14-3
PROPOSALS FOR BEAMTIME ON THE ESRF Bio-SAXS BEAMLINE ID14-3 User operation on the new Bio-SAXS beamline at ID14-3 at the ESRF ( http://www.esrf.fr/UsersAndScience/Experiments/MX/About_our_beamlines/copy_of_ID14-3 ) began in November 2008 with mounting of samples currently performed manually. Robotic sample loading will be incorporated on the beam-line in the coming months using a device being constructed in a collaboration between the EMBL (Grenoble and Hamburg outstations) and the ESRF. Automated data analysis will be also implemented following the model of the SAXS facility at X-33, EMBL Hamburg. Eventually the end-station will be fully automated (sample loading, data collection, processing and preliminary analysis) and will rapidly provide users standard data concerning the size (radius of gyration, maximum dimension and volume) and molecular weight of samples and allow on-the fly ab-initio shape reconstruction in order to provide feedback enabling the data collection strategies to be optimized. Future plans extend to allowing remote access to the new Bio-SAXS facility, based on the system currently in use on the ESRF's MX end-stations. Application for beam-time on the new facility will follow a rapid access model and can be made at ANY time. Those who which to apply (including members of ESRF MX BAG Groups) should use the mechanism at: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal where it must be clearly indicated in the title of the proposal that the application is for Bio-SAXS beamtime on ID14-3.
[ccp4bb] CALL FOR PROPOSALS FOR ESRF BEAMTIME WITH ONLINE MICROSPEC
CALL FOR PROPOSALS FOR BEAMTIME WITH ONLINE MICROSPEC Proposal Deadline 31st January 2009 There will be beamtime available at the ESRF for MX data collection with a setup that allows online monitoring of UV/VIS spectral changes of the crystal during the X-ray diffraction experiment. Users who are interested in using this beam time (including those who are members of BAG Groups) should use the following mechanism: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal and it must be clearly indicated in the title of the proposal form that the online monitoring of spectral changes is necessary for the project. A brief description of the device is given below however users are encouraged to consult the web pages for detailed information: http://www.esrf.fr/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/Run_Your_Experiment/Microspectrophotometer_User_Guide As this is not a standard setup, it might take a significant amount of time to train users, align the device, and analyse the data in order to derive relevant data collection schemes. We will therefore schedule 24 hours for each project. The deadline for this specific application is Saturday 31st January 2009 *Dates of beam-time: 20th - 23rd February 2009 *Storage Ring: 7/8 +1 (200mA) Beamline: ID14-2 Energy: 13.29 keV Specifications: UV/VIS-range: 250-800nm ODmax: 2-2.5 min integration time: 50ms Light source: OceanOptics DH2000, Halogen/D2-lamp Monitoring Light size: 0.03 (min) - 0.15mm(max) Sampling freq (to disk): 10Hz or lower -- Dr Didier NURIZZO MX Beam-Line Operations Manager Tel : (+33) 4 76 88 29 00 Macromolecular Crystallography Group Fax : (+33) 4 76 88 26 24 ESRF B.P. 220, 6 rue Jules Horowitz e-mail : nuri...@esrf.fr F-38043 GRENOBLE CEDEX http://www.esrf.fr
[ccp4bb] ESRF School - 2nd - 5th February 2009
Dear all, We are pleased to announce the ESRF School titled *"Getting the most from the ESRF MX beamlines"* ESRF, Grenoble, France, 2nd - 5th February 2009 As part of its 2009 Users Meeting, the ESRF will host a short school *"Getting the most from the ESRF MX beamlines"* from 2nd to 5th February 2009. The School will be held on 3 days either side of the Users Meeting and is aimed at younger, relatively inexperienced users of the ESRF's MX beam-lines. The school is designed to (a) introduce the art of collecting good diffraction data at synchrotron-based MX facilities, (b) familiarize the participants with the tools available at the beam-line to allow correct pre- and post-data collection decisions to be taken and (c) present the various ancillary techniques and equipment accessible at the ESRF’s MX beam-lines. The number of participants will be limited to 20 with all _local costs_ (i.e. registration fees, accommodation, subsistence) being met by the ESRF. The deadline for applications is 15th December 2008. More detailed information, a preliminary programme and instructions as to how to apply to attend the school can be found at: http://www.esrf.fr/events/conferences/usersmeeting2009/mx-school The organising Committee
[ccp4bb] CALL FOR PROPOSALS FOR BEAMTIME WITH ONLINE MICROSPEC
CALL FOR PROPOSALS FOR BEAMTIME WITH ONLINE MICROSPEC Proposal Deadline *1st March 2008 *There will be beamtime available at the ESRF for MX data collection with a setup that allows online monitoring of UV/VIS spectral changes of the crystal during the X-ray diffraction experiment. Users who are interested in using this beam time (including those who are members of BAG Groups) should using the following mechanism: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal and it must be clearly indicated in the title of the proposal form that the online monitoring of spectral changes is necessary for the project. A brief description of the device is given below however users are encouraged to consult the web pages for detailed information: http://www.esrf.fr/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/Run_Your_Experiment/Microspectrophotometer_User_Guide As this is not a standard setup, it might take a significant amount of time to train users, align the device, and analyse the data in order to derive relevant data collection schemes. We will therefore schedule 24 hours for each project. The deadline for this specific application is Saturday 1st March 2008 *Dates of beam-time: 11th - 14th April 2008 *Storage Ring: 7/8 +1 (200mA) Beamline: ID14-2 Energy: 13.29 keV Specifications: UV/VIS-range: 250-800nm ODmax: 2-2.5 min integration time: 50ms Light source: OceanOptics DH2000, Halogen/D2-lamp Monitoring Light size: 0.03 (min) - 0.15mm(max) Sampling freq (to disk): 10Hz or lower
[ccp4bb] ESRF Rolling access beamtime
Dear all, The ESRF is pleased to remind you about the procedure for applying for rolling access beamtime on its MX beamlines. The rolling access procedure is designed to improve access to ESRF MX beam-lines and encourage the use of ESRF facilities by smaller groups working in the MX field. This method of applying for beam-time can be used by scientists who are NOT included in a ESRF blocked group (BAG) and applications can be made at ANY time. Applications received under this new scheme will be reviewed electronically by the ESRF MX Beam Time Review Committee within 7-14 days of their reception at the ESRF and if beam-time is awarded this will be scheduled within 6-8 weeks after the time of application. The ESRF is currently accepting applications for rolling access beamtime required in January and February 2008. Further details of the scheme as well as details of application procedures are available at: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/MXApplications/#standard Any questions regarding this new application mechanism should be initially directed to Debby Davison ([EMAIL PROTECTED]), or the the MX Beamline Operation Managers (Joanne McCarthy ([EMAIL PROTECTED]) and Didier Nurizzo ([EMAIL PROTECTED]).
[ccp4bb] ESRF Rolling access beamtime
Dear all, The ESRF is pleased to remind you about the procedure for applying for rolling access beamtime on its MX beamlines. The rolling access procedure is designed to improve access to ESRF MX beam-lines and encourage the use of ESRF facilities by smaller groups working in the MX field. This method of applying for beam-time can be used by scientists who are NOT included in a ESRF blocked group (BAG) and applications can be made at ANY time. Applications received under this new scheme will be reviewed electronically by the ESRF MX Beam Time Review Committee within 7-14 days of their reception at the ESRF and if beam-time is awarded this will be scheduled within 6-8 weeks after the time of application. The ESRF is currently accepting applications for rolling access beamtime required in November and December 2007. Further details of the scheme as well as details of application procedures are available at: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/MXApplications/#standard Any questions regarding this new application mechanism should be initially directed to Debby Davison ([EMAIL PROTECTED]), or the the MX Beamline Operation Managers (Joanne McCarthy ([EMAIL PROTECTED]) and Didier Nurizzo ([EMAIL PROTECTED]).
[ccp4bb] ESRF Rolling access beamtime
The ESRF is pleased to remind you about the procedure for applying for rolling access beamtime on its MX beamlines. The rolling access procedure is designed to improve access to ESRF MX beam-lines and encourage the use of ESRF facilities by smaller groups working in the MX field. This method of applying for beam-time can be used by scientists who are NOT included in a ESRF blocked group (BAG) and applications can be made at ANY time. Applications received under this new scheme will be reviewed electronically by the ESRF MX Beam Time Review Committee within 7-14 days of their reception at the ESRF and if beam-time is awarded this will be scheduled within 6-8 weeks after the time of application. The ESRF is currently accepting applications for rolling access beamtime required in September and October 2007. Further details of the scheme as well as details of application procedures are available at: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/MXApplications/#standard Any questions regarding this new application mechanism should be initially directed to Debby Davison ([EMAIL PROTECTED]), or the the MX Beamline Operation Managers (Joanne McCarthy ([EMAIL PROTECTED]) and Didier Nurizzo ([EMAIL PROTECTED]).
