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@phenix-online.org> <phenixbb-request@phenix-online.org> wrote:
>
> Message: 5
> Date: Mon, 19 Oct 2015 11:16:17 -0500
> From: Murpholino Peligro <murpholinox@gmail.com>
> To: PHENIX user mailing list <phenixbb@phenix-online.org>
> Subject: [phenixbb] How to convert XDS_ASCII.HKL to MTZ
> Message-ID:
> <CAMdBu0Uejh0k+Wih1KaF+c=FRJ3fKg+LhQrfuGhUs1tJ8x8HwQ@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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