On Tuesday, February 12, 2013 09:52:19 am Phil 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.
Pointless changes the Fs to Is, so you need to get back to Fs somehow.
Ethan
> Maybe use old truncate with the notruncate option
> Phil
>
> Sent from my iPad
>
> On 12 Feb 2013, at 18:48, Ethan Merritt <[email protected]> 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 <[email protected]> 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
