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. > >
