Hi, everyone Now I can get collect result after setting ORGX and ORGY to 1024. Thank Manfred for his help. Thank everyone who helped me.
Best regard Chang > > 2012/10/29 Manfred S. Weiss <[email protected]>: >> The same is true for the third data. I would suggest the following. >> Examine the images and try to see where the origin is. If you >> cannot figure this out, set ORGX and ORGY both to 1024, which >> is the exact center of the detector. And then try again and send >> me the IDXREF.LP >> >> >> Best wishes >> >> Manfred >> >> On 29.10.2012 08:35, Chang Qing wrote: >>> >>> 2012/10/29 Chang Qing <[email protected]>: >>>> >>>> 2012/10/29 Chang Qing <[email protected]>: >>>>> >>>>> Thank you very much. I will send you the files through three mail. >>>>> >>>>> 2012/10/29 Manfred S. Weiss <[email protected]>: >>>>>> >>>>>> Thank you very much. I think this is a trivial error, but I will have >>>>>> to >>>>>> investigate >>>>>> a little bit. Can you also send me the files IDXREF.LP and FRAME.cbf >>>>>> for the >>>>>> three data sets processed with XDS? >>>>>> >>>>>> Of course I will treat your data in confidence. >>>>>> >>>>>> With best wishes >>>>>> >>>>>> Manfred >>>>>> >>>>>> >>>>>> On 29.10.2012 07:54, Chang Qing wrote: >>>>>>> >>>>>>> 2012/10/29 Chang Qing <[email protected]>: >>>>>>>> >>>>>>>> 2012/10/29 Chang Qing <[email protected]>: >>>>>>>>> >>>>>>>>> Dear Manfred >>>>>>>>> >>>>>>>>> Thank you very much. I think I cannot answer your questions in >>>>>>>>> detail. >>>>>>>>> As I am a clinical doctor indeed, I don't know some principles in >>>>>>>>> detail. I will send you all log file. >>>>>>>>> Mail will be separated in three. >>>>>>>>> First letter, data is collected in spring8(41xu), and can get >>>>>>>>> correct >>>>>>>>> result. >>>>>>>>> Second and third letter, date is collected in KEK(nw12a), and space >>>>>>>>> group are wrong. >>>>>>>>> As my data is not publication yet, would you please keep it secret? >>>>>>>>> Thank you very much. >>>>>>>>> As I use macbook, XDSAPP cannot be installed on it. >>>>>>>>> >>>>>>>>> 2012/10/29 Manfred S. Weiss <[email protected]>: >>>>>>>>>> >>>>>>>>>> Dear Chang, >>>>>>>>>> >>>>>>>>>> there is something seriously wrong with this data. It is possible >>>>>>>>>> that >>>>>>>>>> the >>>>>>>>>> lattice is mis-indexed. Which images did you use for indexing. In >>>>>>>>>> contrast >>>>>>>>>> to HKL2000, which indexes based on a Fourier analysis of just one >>>>>>>>>> images, XDS indexes based on differences vector and needs at least >>>>>>>>>> a few (10) images, better would be two slices of 10 images 90 >>>>>>>>>> degrees >>>>>>>>>> apart. >>>>>>>>>> >>>>>>>>>> Which XDS tutorial have you followed? Have you tried any of the >>>>>>>>>> automatic >>>>>>>>>> versions of XDS, such as XDSAPP which we are developing in our lab? >>>>>>>>>> >>>>>>>>>> Where were the data collected? If you send me some more information >>>>>>>>>> about your data I will help you process them using XDS. >>>>>>>>>> >>>>>>>>>> With best regards >>>>>>>>>> >>>>>>>>>> Manfred >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 29.10.2012 06:03, Chang Qing wrote: >>>>>>>>>>> >>>>>>>>>>> And CORRECT file >>>>>>>>>>> >>>>>>>>>>> 2012/10/29 Chang Qing <[email protected]>: >>>>>>>>>>>> >>>>>>>>>>>> Here, I show some information about my data and input files of >>>>>>>>>>>> XDS. >>>>>>>>>>>> >>>>>>>>>>>> Wavelength (A) 1.0000 >>>>>>>>>>>> Raster size (mm) 0.10240 (default) >>>>>>>>>>>> Raster size (mm) 0.10240 (default) >>>>>>>>>>>> Film width (mm) 209.72 (default) >>>>>>>>>>>> Film length (mm) 209.72 (default) >>>>>>>>>>>> Record length (pixels) 2048 (default) >>>>>>>>>>>> Number of records 2048 (default) >>>>>>>>>>>> Top limit of useful data 0.0000 (default) >>>>>>>>>>>> Left limit of useful data 0.0000 (default) >>>>>>>>>>>> spots rejected when pixel overflow at value : 65500.0 >>>>>>>>>>>> pixels rejected at value: 0 >>>>>>>>>>>> Oscillation starts at 0.0000 >>>>>>>>>>>> Oscillation range 1.0000 >>>>>>>>>>>> Lattice type: primitive >>>>>>>>>>>> Orientation axis 1 (vertical plane) 1*h 0*k 0*l (default) >>>>>>>>>>>> Orientation axis 2 (spindle) 0*h 0*k 1*l (default) >>>>>>>>>>>> Mosaicity 0.30000 >>>>>>>>>>>> CrysZ (beam) axis 0.0000 (default) >>>>>>>>>>>> CrysY (vertical) axis 0.0000 (default) >>>>>>>>>>>> CrysX (spindle) axis 0.0000 (default) >>>>>>>>>>>> unit cell parameters not entered >>>>>>>>>>>> Detector (mis)orientation angles: >>>>>>>>>>>> CassZ (beam) axis 0.0000 >>>>>>>>>>>> CassY (vertical) axis 0.0000 >>>>>>>>>>>> CassX (spindle) axis 0.0000 >>>>>>>>>>>> Detector 2 theta 0.0000 >>>>>>>>>>>> Detector rotation 90.000 (default) >>>>>>>>>>>> Flat detector (default) >>>>>>>>>>>> Detector to crystal distance 166.20 >>>>>>>>>>>> X beam 104.80 >>>>>>>>>>>> Y beam 105.10 >>>>>>>>>>>> Beam polarization 0.99000 >>>>>>>>>>>> Detector absorption 100.00 (default) >>>>>>>>>>>> Air absorption length 860.00 (default) >>>>>>>>>>>> Crossfire y 0.0000 >>>>>>>>>>>> Crossfire x 0.0000 >>>>>>>>>>>> Crossfire xy 0.0000 >>>>>>>>>>>> Horizontal box size 3.6864 >>>>>>>>>>>> Vertical box size 3.6864 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> 2012/10/29 Zhijie Li <[email protected]>: >>>>>>>>>>>>> >>>>>>>>>>>>> BTW, did you supply XDS with correct beamline/detector >>>>>>>>>>>>> information >>>>>>>>>>>>> in >>>>>>>>>>>>> your >>>>>>>>>>>>> input file? Have you compared these information with your >>>>>>>>>>>>> HKL2000 >>>>>>>>>>>>> site >>>>>>>>>>>>> file? >>>>>>>>>>>>> If you show us the input file and the HKL2000 site file it might >>>>>>>>>>>>> be >>>>>>>>>>>>> helpful. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -------------------------------------------------- >>>>>>>>>>>>> From: "Chang Qing" <[email protected]> >>>>>>>>>>>>> Sent: Monday, October 29, 2012 12:06 AM >>>>>>>>>>>>> To: "Zhijie Li" <[email protected]> >>>>>>>>>>>>> Subject: Re: [ccp4bb] How to start my XDS journey after HKL2000? >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> There were no obvious error messages after XDS. Just, the >>>>>>>>>>>>>> result of >>>>>>>>>>>>>> space group was wrong. I can not solve structure through wrong >>>>>>>>>>>>>> space >>>>>>>>>>>>>> group. Quality of data is very good. I thought I could get >>>>>>>>>>>>>> correct >>>>>>>>>>>>>> result even parameters were in default as recommended in >>>>>>>>>>>>>> tutorial. >>>>>>>>>>>>>> I >>>>>>>>>>>>>> was confused so much. >>>>>>>>>>>>>> >>>>>>>>>>>>>> 2012/10/29 Zhijie Li <[email protected]>: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> You had better also include some error message. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -------------------------------------------------- >>>>>>>>>>>>>>> From: "Chang Qing" <[email protected]> >>>>>>>>>>>>>>> Sent: Sunday, October 28, 2012 10:40 PM >>>>>>>>>>>>>>> To: <[email protected]> >>>>>>>>>>>>>>> Subject: [ccp4bb] How to start my XDS journey after HKL2000? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi all >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Now, I am studying XDS. I have 2 sets of data, which can >>>>>>>>>>>>>>>> correctly >>>>>>>>>>>>>>>> treated by HKL2000 and the results are very good. I followed >>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>> tutorial of XDS, but got wrong space group. Inputing the >>>>>>>>>>>>>>>> correct >>>>>>>>>>>>>>>> space >>>>>>>>>>>>>>>> group was helpless. Results of pointless were also wrong, and >>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>> not pass scala. Can someone give me some recommendation? >>>>>>>>>>>>>>>> Thanks. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Chang >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Dr. Manfred. S. Weiss >>>>>>>>>> Helmholtz-Zentrum Berlin für Materialien und Energie >>>>>>>>>> Macromolecular Crystallography (HZB-MX) >>>>>>>>>> Albert-Einstein-Str. 15 >>>>>>>>>> D-12489 Berlin >>>>>>>>>> GERMANY >>>>>>>>>> Fon: +49-30-806213149 >>>>>>>>>> Fax: +49-30-806214975 >>>>>>>>>> Web: http://www.helmholtz-berlin.de/bessy-mx >>>>>>>>>> Email: [email protected] >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ________________________________ >>>>>>>>>> >>>>>>>>>> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH >>>>>>>>>> >>>>>>>>>> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher >>>>>>>>>> Forschungszentren >>>>>>>>>> e.V. >>>>>>>>>> >>>>>>>>>> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim >>>>>>>>>> Treusch, >>>>>>>>>> stv. >>>>>>>>>> Vorsitzende Dr. Beatrix Vierkorn-Rudolph >>>>>>>>>> Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas >>>>>>>>>> Frederking >>>>>>>>>> >>>>>>>>>> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >>>>>>>>>> >>>>>>>>>> Postadresse: >>>>>>>>>> Hahn-Meitner-Platz 1 >>>>>>>>>> D-14109 Berlin >>>>>>>>>> >>>>>>>>>> http://www.helmholtz-berlin.de >>>>>> >>>>>> >>>>>> -- >>>>>> Dr. Manfred. S. Weiss >>>>>> Helmholtz-Zentrum Berlin für Materialien und Energie >>>>>> Macromolecular Crystallography (HZB-MX) >>>>>> Albert-Einstein-Str. 15 >>>>>> D-12489 Berlin >>>>>> GERMANY >>>>>> Fon: +49-30-806213149 >>>>>> Fax: +49-30-806214975 >>>>>> Web: http://www.helmholtz-berlin.de/bessy-mx >>>>>> Email: [email protected] >>>>>> >>>>>> >>>>>> ________________________________ >>>>>> >>>>>> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH >>>>>> >>>>>> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher >>>>>> Forschungszentren >>>>>> e.V. >>>>>> >>>>>> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, >>>>>> stv. >>>>>> Vorsitzende Dr. Beatrix Vierkorn-Rudolph >>>>>> Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas >>>>>> Frederking >>>>>> >>>>>> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >>>>>> >>>>>> Postadresse: >>>>>> Hahn-Meitner-Platz 1 >>>>>> D-14109 Berlin >>>>>> >>>>>> http://www.helmholtz-berlin.de >> >> >> -- >> Dr. Manfred. S. Weiss >> Helmholtz-Zentrum Berlin für Materialien und Energie >> Macromolecular Crystallography (HZB-MX) >> Albert-Einstein-Str. 15 >> D-12489 Berlin >> GERMANY >> Fon: +49-30-806213149 >> Fax: +49-30-806214975 >> Web: http://www.helmholtz-berlin.de/bessy-mx >> Email: [email protected] >> >> >> ________________________________ >> >> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH >> >> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren >> e.V. >> >> Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. >> Vorsitzende Dr. Beatrix Vierkorn-Rudolph >> Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking >> >> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >> >> Postadresse: >> Hahn-Meitner-Platz 1 >> D-14109 Berlin >> >> http://www.helmholtz-berlin.de
