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
