I have a question regarding model building. can anyone guide how to find and add water molecules in electron density map in coot. regardsSaleem
> Date: Mon, 29 Oct 2012 19:23:00 +0900 > From: [email protected] > Subject: Re: [ccp4bb] How to start my XDS journey after HKL2000? > To: [email protected] > > 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
