Hi > I had processed the images using iMOSFLM. The option of “automatic ice and > powder ring exclusion” was toggled ON when I processed the data. It is only > now I realize that this is not the way to get rid of ice rings. > This is due to the exclusion limits being set too conservatively for the ice rings; you might consider it a bug, because this should be the way to get rid of the ice rings! > The latest paper on the use of iMOSFLM (Powell. H. R et al, Nature Protocols, > 2017) suggests excluding data within specific resolution shells to get rid of > the ice ring problem. I observe that if I set the limits 3.62-3.68, > 2.23-2.26, 1.90-1.93 Å in “excluded resolution ranges” option of iMOSFLM, > only the spots upto 3.6 Å are found and also predicted. Moreover all high > resolution data is lost. Somehow I am not able to get this strategy working > in iMOSFLM. >
This is due to a bug in the iMosflm code; it will be fixed in the next release (I've told the current developer about it...). I could send you a fix so that this option works if you like. Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 9 Aug 2017, at 13:17, Satvik Kumar wrote: > Dear All, > > > > Thank you all for your inputs. > > > > You are all correct. The diffraction images have ice rings at 3.67, 2.24 and > 1.9 Å. The intensity of these ice rings decrease with increasing resolution. > In the Wilson plot, I clearly observe the spikes in intensity corresponding > to these resolutions. > > > > > > The latest paper on the use of iMOSFLM (Powell. H. R et al, Nature Protocols, > 2017) suggests excluding data within specific resolution shells to get rid of > the ice ring problem. I observe that if I set the limits 3.62-3.68, > 2.23-2.26, 1.90-1.93 Å in “excluded resolution ranges” option of iMOSFLM, > only the spots upto 3.6 Å are found and also predicted. Moreover all high > resolution data is lost. Somehow I am not able to get this strategy working > in iMOSFLM. > > > > The other suggestion was to deice using AUSPEX or DEICE. The information > available on the internet suggests AUSPEX is a diagnostic tool. Is it > possible to use it to deice? I will be trying to get DEICE working shortly. > > > > Please share your thoughts as to how I should proceed. > > > Thanks, > > Satvik > > > On Tue, Aug 8, 2017 at 11:47 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > You have some horrible ice rings - some data processing software may be able > to cut them out.. how are you processing it? > Eleanor > > On 8 August 2017 at 15:43, Christian Roth <christianroth...@gmail.com> wrote: > Your plots look strangely different to the old Scala output you posted > before, but never mind. > > Paul is right that a negative intensity is not desired and your crystal has > some issues with ice. > > That one icering around 2.26 must be massive taken into account how haywire > your curve goes there. > > Have you had a look at the images? There should be something visible in that > area. > > Christian > > > Am 08.08.2017 um 15:17 schrieb Paul Emsley: >> On 08/08/2017 15:07, Satvik Kumar wrote: >>> Dear Prof. Powell and Prof. Dodson, >>> >>> Thanks for your reply and advise. >>> >>> As per your suggestion, I have re-scaled the intensities using Aimless at >>> 1.861 A. >>> >>> I observe that the I/sigI has dropped to -0.8 >> >> That's not good. >> >> > and the behaviour of CC_1/2 is still anomalous. >> >> That made me laugh out loud. Perhaps not the best choice of adjective. >> >>> >>> Also, when I inspect the Wilson plot (Fig. 1), I observe that the curve >>> does not fall smoothly with respect to the reference curve (blue). Even >>> with respect to one more Wilson plot from CCP4 website (Fig. 2), the curve >>> from my aimless output is different and discontinuous. >> >> Icy! >> >> /me wonders if CCP4 are distributing auspex yet... >> >>> >>> The second moment of I is constant only up to a resolution of 2.4 Å at a >>> value of 3 (Fig. 3). I was not able to get some other plot to compare >>> against mine. >>> >>> Please tell me if I can still go ahead and refine at 1.861 A. >> >> No you can't. >> >> Maybe with some chopping you can rescue some reflections beyond 2.1. >> >> Paul >> > > > > <090817.pdf>
