<div dir="ltr">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. <br><br>I can see that XDSCONV has by default NEGATIVE_INTENSITY_CUTOFF=-3. Does phenix.reflection_file_converter have a similar default?<br><br><br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-10-19 11:28 GMT-05:00 Whitley, Matthew J <span dir="ltr"><<a href="mailto:mjw100@pitt.edu" target="_blank">mjw100@pitt.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Murpholino,<br>
<br>
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.)<br>
<br>
You can find step by step instructions for generating an MTZ file from XDS output under the “Typical Use” heading here:<br>
<a href="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv" rel="noreferrer" target="_blank">http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv</a><br>
<br>
More info about XDSCONV:<br>
<a href="http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_parameters.html" rel="noreferrer" target="_blank">http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_parameters.html</a><br>
<br>
Good luck!<br>
Matthew<br>
<br>
<br>
<br>
On Oct 19, 2015, at 12:16 PM, <<a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a>> <<a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a>> wrote:<br>
<br>
><br>
> Message: 5<br>
> Date: Mon, 19 Oct 2015 11:16:17 -0500<br>
> From: Murpholino Peligro <<a href="mailto:murpholinox@gmail.com">murpholinox@gmail.com</a>><br>
<span class="">> To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
> Subject: [phenixbb] How to convert XDS_ASCII.HKL to MTZ<br>
</span>> Message-ID:<br>
> <CAMdBu0Uejh0k+Wih1KaF+c=<a href="mailto:FRJ3fKg%2BLhQrfuGhUs1tJ8x8HwQ@mail.gmail.com">FRJ3fKg+LhQrfuGhUs1tJ8x8HwQ@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
<span class="">><br>
> Just want to be sure.<br>
> I want to generate the mtz file for refinement. The last step of XDS leaves<br>
> me with intensities and space group 89. So I need<br>
><br>
> phenix.reflection_file_converter --generate-r-free-flags<br>
> --write-mtz-amplitudes --mtz_root_label=FOBS --mtz=d01.mtz<br>
> --change-to-space-group=96 XDS_ASCII.HKL<br>
><br>
> Is this right?<br>
><br>
> Thanks again<br>
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