Dear Almudena,
Let me give you a bit more guidance regarding the files of interest.
The main user-oriented output from autoPROC is the "summary.html" file.
Numerous files are linked from within that html file, that are not meant to
be looked at individually with bare hands. This summary documents the steps
followed by autoPROC, and the final section "Finalising output" has all the
information you need as to what files contain what, with links to them so
that you can easily download them without having to inspect directories
yourself.
It is the final sub-section, annotated "anisotropic", that contains
these links, as well as a printed Table 1. The file you want is called
"staraniso_alldata-unique.mtz". If you just used the XDS_ACII.HKL you would
forfeit the extra treatment by STARANISO. There is a "table1" link to the
contents, as a separate text file, of the box shaded in light green in the
summary file, and a link "xml" with this information in XML form for
harvesting by synchrotron auto-processing pipelines. You will also find a
link "Data_1_autoPROC_STARANISO_all.cif" that directs you to an mmCIF file
containing the final data, ready for deposition into the PDB. Finally, for
good measure, there is link to a full PDF report of the autoPROC results,
called "report_staraniso.pdf".
I hope this guidance is of some help. The main message is: look at the
summary.html file.
It has been clear for some time that users expect to be able to use
programs without having to look at the documentation, but it is a relatively
new development that they expect to be able to use the results without
having to look at any output :-) .
With best wishes,
Gerard.
--
On Sat, Nov 07, 2020 at 10:06:58PM +0000, Gerard Bricogne wrote:
> Dear Almudena,
>
> I am glad that you got some helpful responses by writing to the ccp4bb
> about your problem, and would like to thank those who sent them.
>
> Please note, however, that there is a user support mailing list for
> autoPROC, called "[email protected]", where such questions will
> always be welcome and will be answered by the developers themselves.
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Sat, Nov 07, 2020 at 08:45:39PM +0100, Almudena Ponce Salvatierra wrote:
> > Hi Kay, Michal, Guillermo,
> >
> > thank you all for your answers.
> >
> > @Kay Diederichs <[email protected]> and Michal, indeed I tried
> > with the XDS outputs first, since this is what I'm most familiar with.
> > However, when I load them in Xtriage to see how the data is going to look
> > overall, I see that only I, SIGI are there. See the screenshot attached.
> >
> > @Guillermo Montoya <[email protected]> I am trying! :) My images
> > are from a Pilatus detector, in cbf format. Is what you sent in this later
> > email equivalent to "process -I Directory_1_002 -I Directory_1_003 -I
> > Directory_1_004 -I Directory_1_005 -I Directory_1_006 -I Directory_1_007 -I
> > Directory_1_008 -I Directory_1_009 -d 0comb -ANO"
> >
> > You wrote -*Id* directory/image...cbf but I was not able to run it like
> > that... so I used -I... it's running now.
> >
> > Thank you very much everyone. Have a nice Saturday evening!
> >
> > Best,
> >
> > Almu
> >
> > El sáb., 7 nov. 2020 a las 20:09, Kay Diederichs (<
> > [email protected]>) escribió:
> >
> > > Hello Almudena,
> > >
> > > XDS_ASCII.HKL _has_ all the information. Whether the HKL values of a given
> > > record of that file refer to I(+) or I(-) is worked out by the scaling
> > > program.
> > >
> > > HTH,
> > > Kay
> > >
> > > On Sat, 7 Nov 2020 19:07:59 +0100, Almudena Ponce Salvatierra <
> > > [email protected]> wrote:
> > >
> > > >Hello everyone,
> > > >
> > > >I am using autoPROC in a series of datasets I referred to in an email a
> > > few
> > > >days ago.
> > > >
> > > >I would like to merge them and see if the resulting dataset has enough
> > > >anomalous signal as to phase.
> > > >
> > > >The thing is that, out of the massive output from autoPROC, I fail to
> > > >find
> > > >which files to merge. I am using the command "combine_files -f ... -f ...
> > > >-o combined.mtz". But neither aimless_unmerged.mtz or XDS_ASCII.HKL
> > > >files,
> > > >seem to contain any record of I(+)I(-) etc...
> > > >
> > > >I'll be very thankful for any suggestions.
> > > >
> > > >Best,
> > > >
> > > >Almudena
> > > >
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