Hi,
I do this by editor (and cut / paste). Clumsy but works. Let me know if you find a more elegant way.
Cheers,
Boaz
-------- Original message --------
From: Wei Wang <ww2...@columbia.edu>
Date: 21/11/2016 19:05 (GMT+02:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] XDS questions
My personal test shows that the different paths vary little with each other, as long as the scaling is done only once. Another way could be what is said on XDSwiki: Minimum I/Sigma=50, CORRECTIONS=MODULATION, NBATCH=1. Then the XDS_ASCII.HKL is handed
over to Aimless with default settings.
One question raised is that how can I move the 'aliens' with Z>20 to REMOVE.HKL? I didn't find answer yet. Maybe I didn't read carefully over the documents, but I would appreciate it if someone can teach me.On Mon, Nov 21, 2016 at 6:13 AM, Tim Gruene
<tim.gru...@psi.ch> wrote:
Dear Nishant,
XDS_ASCII.HKL contains corrected, scaled, but not merged reflections.
You can specifically ask XDS to merge your data, but I would not do so unless
really necessary - you loose a lot of information.
I would like to offer a different opinion to Graeme's:
You can read XDS_ASCII.HKL into pointless and aimless and provide aimless with
the option 'onlymerge'. This way aimless merges the data, but it does not
rescale them.
XDS performs a couple of corrections in the CORRECT step, the output of which
is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not sure
aimless takes into account how XDS treats the data. I would therefore trust
the step of scaling to the same author and continue with XDS_ASCII.HKL.
Best,
Tim
--
On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
> Dear All,
>
> Just to understand more, the XDS_ASCII.HKL file generated after running XDS
> contains scaled and merged reflections?
>
> Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS
> instead of INTEGRATE.HKL file??
>
> I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and
> another using INTEGRATE.HKL and I found that in the run using XDS_ASCII.HKL
> little lesser total number of observation but marginally better statistics.
>
> Thanks
> Nishant
>
> On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster <docandr...@gmail.com>
>
> wrote:
> > Dear Wei,
> >
> > if you process your data with XDS, the best is probably to do the scaling
> > in XDS (CORRECT) and be done with it. If you want to use Aimless for
> > merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES
> > CONSTANT.
> >
> > All best.
> >
> >
> > Andreas
> >
> > On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang <ww2...@columbia.edu> wrote:
> >> Hi,
> >>
> >> Is there a way to let xds_par use less than all processors/threads on the
> >> machine? Sometimes I would like to process something else while XDS is
> >> running.
> >>
> >> Another question is related to the scaling procedure. My understanding is
> >> that the XDS already does the scaling during correction. So if I follow
> >> the
> >> XDS-Aimless route, then probably I should let Aimless do "skip scaling
> >> and
> >> only merge"? Please elucidate me on this issue.
> >>
> >> Regards,
> >>
> >> Wei
>
> --
> Dr. Nishant Kumar Varshney,
> IISc-ICTP Fellow
> XRD2 Beamline, Elettra-Sincrotrone,
> In Area Science Park,
> Basovizza, S.S. 14, Km 163,5,
> 34012 Trieste, Italy
> +39-040-375 8737 (office ESP4 P1 031)
> +39-040-375-8435 (XRD2 beamline)
> +39 3318809798 (Mobile)
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI
Phone: +41 (0)56 310 5297
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