Hi Phil, what I tend to do if I want to stay as close as possible to the original data:
scala hklin some.mtz hklout tmp.mtz <<end_ip RUN 1 BATCH 1 TO 9999 ONLYMERGE ANALYSE NONORMAL NOPLOT SDCORR NOREFINE FIXSDB NOADJUST BOTH 1.0 0.0 0.0 INITIAL UNITY REJECT 999.9 ALL 999.9 END end_ip truncate hklin tmp.mtz hklout other.mtz <<end_ip SCALE 1.0 ANOM NO END end_ip ... maybe with NOTRUNCATE as well. This is a bit older ... so there might be a way of achieving the same with the more modern aimless and ctruncate? Cheers Clemens On Tue, Feb 12, 2013 at 06:52:19PM +0100, Phil Evans wrote: > 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 -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
