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@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@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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