Dr. Harry, Thank you very much for the illustration!
On Wed, Feb 15, 2017 at 2:07 PM, Harry Powell <ha...@mrc-lmb.cam.ac.uk> wrote: > Hi > > First things first... > > 2. I am not sure if iMosflm can be set to output the scale of specific > space group. For example, in my data set even though the integration is > done at P321 space group, after click "quick symm" or "quick scale" it > seems the program automatically choose what it thinks the most likely space > group P6222, not P321, I know in HKL2000 there is an option to choose > specific group and scale it, how to do this in iMosflm? I'd like to scale > the data to P321 and some subgroups in P3 but not P6222. > > > Yes, easily done. In the Indexing task, at the bottom left where iMosflm > chooses the space group for you, there's a drop-down where you can pick any > of the chiral trigonal or hexagonal space groups. You could even, if you > wanted, type in any of the achiral space groups and that would work too. > > HOWEVER, unless you are using the Strategy option, I really wouldn't > bother doing this (most of the time). The *measured* reflections for both > trigonal and hexagonal space groups are the in the same places and the > extra symmetry you would have from hexagonal is ignored in the integration. > The QuickScale option will let Pointless do its job and give you a better > analysis of the true symmetry and also apply the symmetry to your MTZ file > (Pointless will use the intensities in its calculations, which is not > something that Mosflm does). > > Importing the output MTZ file from iMosflm (if you haven't run QuickScale) > into either ccp4i or ccp4i2 will also run Pointless and try to sort out > your symmetry for you. > > Does this mean if I see twist variance greater than "1" then I need to > fix both "tilt' and "twist" value before integration in imosflm? > > > Yes, generally speaking if you fix tilt you would probably want to fix > twist as well. > > In my case the variance is greater than 0.5 but less than 1, do I still > need to fix both "tilt" and "twist" value > > > Maybe, probably. It's hard to be definitive without seeing the graphs from > integration or the full log file output. > > Try it and see if the merging stats look better... > > Harry > -- > Dr Harry Powell > Chairman of International Union of Crystallography Commission on > Crystallographic Computing > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) > > On 15 Feb 2017, at 16:36, Xiao Lei <xiaolei...@gmail.com> wrote: > > Dear CCP4bb members, > > I have two questions about imosflm integration and scaling process (my > data is 3A resolution and 0.5 degree mosaicity): > > 1. I have warnings after integration saying the twist variance is too > large (from -0.26 to 0.33, which is larger than 0.5), suggesting that cell > parameters may be wrong, and reindex to the right space group may be > needed. After I read the imosflm tutorials from internet, the tutorials > says "For weak images the tilt and twist may not be well defined, and might > refine to large values (greater than one degree). In such cases these > parameters should be fixed. It is not generally recommended to fix any > other detector parameters." > > Does this mean if I see twist variance greater than "1" then I need to > fix both "tilt' and "twist" value before integration in imosflm? In my > case the variance is greater than 0.5 but less than 1, do I still need to > fix both "tilt" and "twist" value? > > 2. I am not sure if iMosflm can be set to output the scale of specific > space group. For example, in my data set even though the integration is > done at P321 space group, after click "quick symm" or "quick scale" it > seems the program automatically choose what it thinks the most likely space > group P6222, not P321, I know in HKL2000 there is an option to choose > specific group and scale it, how to do this in iMosflm? I'd like to scale > the data to P321 and some subgroups in P3 but not P6222. > > > Thanks for any inputs. > > >
