Why do you like P21212 better than P22121? JPK
On Mon, May 7, 2012 at 4:00 PM, Phil Jeffrey <pjeff...@princeton.edu> wrote: > The program that does the indexing in HKL is Denzo. Denzo doesn't care > about the space group. It cares about the point group (cf. Ethan's point) > and the cell dimensions, because it integrates the data without regard to > the symmetry expressed in the intensities - however it does take notice of > the restrictions placed on cell dimensions by point groups. Denzo > therefore picks primitive orthorhombic cells in a<b<c. > > Scalepack scales the integrated data but does not reindex the data if you > tell it the space group is P22121. Therefore unit cell choice in HKL is by > default driven by cell edge size. Scalepack has the ability to reindex the > data, for those of us that like to work in P21212 rather than P22121. > > > On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt > > Scaling is done in a point group, not a space group. > > My quibble with this statement is that the output reflection data from > Scalepack differs depending on what space group you tell it, since > systematic absences along h00, 0k0 and 00l in P2x2x2x are not written out. > The number of reflections affected is quite small, of course. > > > Phil Jeffrey > Princeton > > > > > > On 5/7/12 4:48 PM, Jacob Keller wrote: > >> Is it true that HKL adopts the naming convention of putting the screw >> axes first and then naming a<b<c if possible, whereas CCP4 just makes >> the cell a<b<c? E.g., would HKL ever output by default a p22121 dataset, >> or would it automatically be p21212? >> >> JPK >> >> On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt <merr...@u.washington.edu >> <mailto:merritt@u.washington.**edu <merr...@u.washington.edu>>> wrote: >> >> On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: >> > Hi all, >> > I was wondering if anyone knows how to convert the P21221 to P21212 >> > spacegroup in HKL2000. I scaled the data set in P21212 in HKL >> 2000 but I >> > got a correct MR solution in P21221 spacegroup. >> >> Shya: >> >> Scaling is done in a point group, not a space group. >> >> The point group P222 contains both space groups P2(1)22(1) and >> P2(1)2(1)2, >> so your original scaling is correct in either case. >> >> It is not clear from your query which of two things happened: >> >> 1) The MR solution kept the same a, b, and c axis assignments but made >> a >> different call on whether each axis did or did not correspond to a >> 2(1) screw. >> In this case you don't need to do anything to your files. Just make >> sure >> that you keep the new space group as you go forward into refinement. >> >> 2) The MR solution kept the orginal screw-axis identifications but >> permuted the axes to the standard setting (non-screw axis is >> labelled "c"). >> In this case you will need to construct a file containing the permuted >> indices. For example, the reflection originally labeled (h=1 k=2 >> l=3) is now >> (h=3 k=1 l=2). There are several programs that can help you do this, >> including the HKL2000 GUI. But you do not need to go back into HKL >> if you don't want to. You could, for example, use the ccp4i GUI to >> select >> -> Reflection Data Utilities >> -> Reindex Reflections >> Define Transformation Matrix by entering reflection transformation >> h=l k=h l=k >> >> >> Ethan >> >> >> > I have a script file that >> > runs with scalepack but was wondering if there is an easier way >> to do it >> > with HKL2000 gui mode. >> > thanks, >> > Shya >> > >> >> -- >> Ethan A Merritt >> Biomolecular Structure Center, K-428 Health Sciences Bldg >> University of Washington, Seattle 98195-7742 >> >> >> >> >> -- >> ********************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> email: j-kell...@northwestern.edu >> <mailto:j-keller2@**northwestern.edu<j-kell...@northwestern.edu> >> > >> ********************************************* >> > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
