[phenixbb] How to convert XDS_ASCII.HKL to MTZ

Whitley, Matthew J mjw100 at pitt.edu
Mon Oct 19 09:28:57 PDT 2015

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:

More info about XDSCONV:

Good luck!

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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