Hi again I've just been looking through the Mosflm source code - in your case the limits you have set (if they worked, but because of a bug they don't) would exclude considerably more data than the default values in Mosflm, so I would be inclined to use the "exclude ice rings during integration" button in iMosflm rather than follow our advice in the Nature Protocols paper.
Sorry if this is a little confusing. 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 13:45, Harry Powell wrote: > 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> >
