Re: [ccp4bb] report mosaicity
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Hongshi, if the numbers do not vary too much, e.g. between 0.2 and 0.6, I would deposit the calculated mean. I would say that the reported mosaicity is not too important a figure for a publication. It is interesting when it comes to data collection and planning your strategy, and may be something to consider if it is very, very large, but for a normal structural study it won't matter too much. Best, Tim On 05/16/2014 01:26 AM, hongshi WANG wrote: Hello everyone, I am gonna report the mosaicity of my data set as required by the journal. I processed the data using HKL2000. So I checked the denzo log file. I found many different mosaicity values. The first one is default input (0.3), the rest are corresponding to specific images. I think the mosaicity value required should be an overall value or averaged value. Could you please let me know how I can get it. Or some other software can determine it. I really appreciate your help and response! Hongshi - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTdcyKUxlJ7aRr7hoRAk+GAKD9+jnmvpV+TFw0t8jtSWXemlKsfgCaA7vn s8YBbU/1ghs+C5cYsJrur/A= =Ra/3 -END PGP SIGNATURE-
Re: [ccp4bb] report mosaicity
Hi I'm sure that a real HKL or Denzo/Scalepack expert will correct me, but my recollection is that you don't use any of the values from Denzo, but the value from Scalepack (see http://www.hkl-xray.com/sites/default/files/HKL2000manual/chapter3/step14-1.htm, for example). On 16 May 2014, at 00:26, hongshi WANG wrote: Hello everyone, I am gonna report the mosaicity of my data set as required by the journal. I processed the data using HKL2000. So I checked the denzo log file. I found many different mosaicity values. The first one is default input (0.3), the rest are corresponding to specific images. I think the mosaicity value required should be an overall value or averaged value. Could you please let me know how I can get it. Or some other software can determine it. I really appreciate your help and response! Hongshi Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] report mosaicity
Dear all, Thanks for all your reply and useful comment on this. Harry, You are right. I think there are individual mosaicity value corresponding to each image from scalepack. Clearly, we can get either average or range for report. best, Hongshi On Fri, May 16, 2014 at 2:26 AM, Harry Powell ha...@mrc-lmb.cam.ac.ukwrote: Hi I'm sure that a real HKL or Denzo/Scalepack expert will correct me, but my recollection is that you don't use any of the values from Denzo, but the value from Scalepack (see http://www.hkl-xray.com/sites/default/files/HKL2000manual/chapter3/step14-1.htm, for example). On 16 May 2014, at 00:26, hongshi WANG wrote: Hello everyone, I am gonna report the mosaicity of my data set as required by the journal. I processed the data using HKL2000. So I checked the denzo log file. I found many different mosaicity values. The first one is default input (0.3), the rest are corresponding to specific images. I think the mosaicity value required should be an overall value or averaged value. Could you please let me know how I can get it. Or some other software can determine it. I really appreciate your help and response! Hongshi Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] report mosaicity
If you refine crystal mosaicity (I assume there is a way to do that in the gui) then scalepack prints out a single value for the crystal (search the logfile for mosaicity) eab On 05/16/2014 12:07 PM, hongshi WANG wrote: Dear all, Thanks for all your reply and useful comment on this. Harry, You are right. I think there are individual mosaicity value corresponding to each image from scalepack. Clearly, we can get either average or range for report. best, Hongshi On Fri, May 16, 2014 at 2:26 AM, Harry Powell ha...@mrc-lmb.cam.ac.uk mailto:ha...@mrc-lmb.cam.ac.uk wrote: Hi I'm sure that a real HKL or Denzo/Scalepack expert will correct me, but my recollection is that you don't use any of the values from Denzo, but the value from Scalepack (see http://www.hkl-xray.com/sites/default/files/HKL2000manual/chapter3/step14-1.htm, for example). On 16 May 2014, at 00:26, hongshi WANG wrote: Hello everyone, I am gonna report the mosaicity of my data set as required by the journal. I processed the data using HKL2000. So I checked the denzo log file. I found many different mosaicity values. The first one is default input (0.3), the rest are corresponding to specific images. I think the mosaicity value required should be an overall value or averaged value. Could you please let me know how I can get it. Or some other software can determine it. I really appreciate your help and response! Hongshi Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] report mosaicity
HKL-2000 has a menu button at the top Report. If you click on that a report is generated with mosaicity range explicitly listed. It is probably not suitable to describe a crystal as having a single mosaicity value because mosaicity may be anisotropic. It should be obvious that a unit cell like 58 x 58 x 150 may have a bigger mosaicity along the 58 directions and a smaller mosaicity along the 150 direction and still have the Bragg reflections spatially separated. Thus, the mosaicity reported/used by diffraction image processing is probably just the best estimate for the mosaicity model used by the algorithm AND the orientation of the crystal in the experiment. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Edward A. Berry [ber...@upstate.edu] Sent: Friday, May 16, 2014 11:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] report mosaicity If you refine crystal mosaicity (I assume there is a way to do that in the gui) then scalepack prints out a single value for the crystal (search the logfile for mosaicity) eab On 05/16/2014 12:07 PM, hongshi WANG wrote: Dear all, Thanks for all your reply and useful comment on this. Harry, You are right. I think there are individual mosaicity value corresponding to each image from scalepack. Clearly, we can get either average or range for report. best, Hongshi On Fri, May 16, 2014 at 2:26 AM, Harry Powell ha...@mrc-lmb.cam.ac.uk mailto:ha...@mrc-lmb.cam.ac.uk wrote: Hi I'm sure that a real HKL or Denzo/Scalepack expert will correct me, but my recollection is that you don't use any of the values from Denzo, but the value from Scalepack (see http://www.hkl-xray.com/sites/default/files/HKL2000manual/chapter3/step14-1.htm, for example). On 16 May 2014, at 00:26, hongshi WANG wrote: Hello everyone, I am gonna report the mosaicity of my data set as required by the journal. I processed the data using HKL2000. So I checked the denzo log file. I found many different mosaicity values. The first one is default input (0.3), the rest are corresponding to specific images. I think the mosaicity value required should be an overall value or averaged value. Could you please let me know how I can get it. Or some other software can determine it. I really appreciate your help and response! Hongshi Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] report mosaicity
Hello everyone, I am gonna report the mosaicity of my data set as required by the journal. I processed the data using HKL2000. So I checked the denzo log file. I found many different mosaicity values. The first one is default input (0.3), the rest are corresponding to specific images. I think the mosaicity value required should be an overall value or averaged value. Could you please let me know how I can get it. Or some other software can determine it. I really appreciate your help and response! Hongshi
