[phenixbb] How to convert XDS_ASCII.HKL to MTZ

Murpholino Peligro murpholinox at gmail.com
Mon Oct 19 10:00:30 PDT 2015


Thanks guys. I am asking with phenix.reflection_file_converter because that
is easier for me. I can make a for loop in the terminal without copying
input files to multiple directories.

I can see that XDSCONV has by default NEGATIVE_INTENSITY_CUTOFF=-3. Does
phenix.reflection_file_converter have a similar default?



2015-10-19 11:28 GMT-05:00 Whitley, Matthew J <mjw100 at pitt.edu>:

> Hi Murpholino,
>
> I’m not sure if your Phenix commands are correct, but you might try using
> the program that comes natively with XDS for converting between file
> formats.  That program is XDSCONV.  (As a side note, I think that some of
> the XDSCONV functions require CCP4 to be installed, so if you don’t have
> CCP4 installed you might need to stick to converting with Phenix.)
>
> You can find step by step instructions for generating an MTZ file from XDS
> output under the “Typical Use” heading here:
> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv
>
> More info about XDSCONV:
>
> http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_parameters.html
>
> Good luck!
> Matthew
>
>
>
> On Oct 19, 2015, at 12:16 PM, <phenixbb-request at phenix-online.org> <
> phenixbb-request at phenix-online.org> wrote:
>
> >
> > Message: 5
> > Date: Mon, 19 Oct 2015 11:16:17 -0500
> > From: Murpholino Peligro <murpholinox at gmail.com>
> > To: PHENIX user mailing list <phenixbb at phenix-online.org>
> > Subject: [phenixbb] How to convert XDS_ASCII.HKL to MTZ
> > Message-ID:
> >       <CAMdBu0Uejh0k+Wih1KaF+c=
> FRJ3fKg+LhQrfuGhUs1tJ8x8HwQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Just want to be sure.
> > I want to generate the mtz file for refinement. The last step of XDS
> leaves
> > me with intensities and space group 89. So I need
> >
> > phenix.reflection_file_converter --generate-r-free-flags
> > --write-mtz-amplitudes --mtz_root_label=FOBS --mtz=d01.mtz
> > --change-to-space-group=96 XDS_ASCII.HKL
> >
> > Is this right?
> >
> > Thanks again
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