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
