Ah I'm not sure about that. It may be possible to tell ctruncate not to do this. Actually if you started with Fs you don't want to truncate the data. Maybe use old truncate with the notruncate option
Phil Sent from my iPad On 12 Feb 2013, at 18:48, Ethan Merritt <merr...@u.washington.edu> wrote: > On Tuesday, February 12, 2013 12:39:57 am Phil wrote: >> "Scale constant" in Aimless or Scala should do it. I should probably make >> that automatic. > > "scale constant" did indeed persuade aimless/scala to run. > However, what seems to have happened is that aimless/scala expanded the > original > [I, SIGI] into [I+, SIGI+] [I-, SIGI-], but all the [I-, SIGI-] entries were > filled in as zero. When ctruncate runs, it segfaults on a divide by zero > error. > If I filter out the +/- columns and run ctruncate again, all is well. > So aside from anything else, I think ctruncate needs some sanity checks for > all-zero columns. > > Ethan > > >> >> I should probably also add a CIF reader to Pointless. Is there a good (easy) >> C++ one out there? >> >> Phil >> >> Sent from my iPad >> >> On 12 Feb 2013, at 08:08, Jens Kaiser <kai...@caltech.edu> wrote: >> >>> Ethan, >>> The last time I attempted similar things, I had to run rotaprep to >>> convince scala of using most things that did not come directly out of >>> mosflm, but that was before the pointless days. >>> As the reflections are already scaled in P1, I would consider it safe >>> to rely on the Pointless Rmerge -- but that's just a guess (and you >>> can't do much with the data downstream). I would assume sftools might be >>> able to merge the reindexed file output by pointless. >>> Nevertheless, if I were faced with the same problem nowadays, I would >>> convert to a shelx hkl file and use xprep for the merging and statistics >>> -- that's "painless". >>> >>> Cheers, >>> >>> Jens >>> >>> On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: >>>> Hi all, >>>> >>>> I've downloaded a structure factor file from the PDB that presents >>>> itself as being triclinic. It contains F, sig(F), and Rfree only. >>>> The P1-ness of this structure is dubious, however. >>>> >>>> Pointless is 99.6% sure it's orthorhombic and puts out an mtz file >>>> in P212121 containing >>>> I SIGI BATCH M/ISYM >>>> >>>> where the batch numbers are all 1 and ISYM runs from 1 to 8. >>>> So far so good, but now I'm stuck. I can't persuade Scala >>>> or Aimless to merge the symmetry mates and report a merging >>>> R factor. Is there a trick to this? Some other program sequence? >>>> >>>> Ethan > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > University of Washington, Seattle 98195-7742
