[phenixbb] How to convert XDS_ASCII.HKL to MTZ

Murpholino Peligro murpholinox at gmail.com
Mon Oct 19 10:34:28 PDT 2015


Besides...if I want to change the space group number with XDSCONV, I'll
need to specify the unit cell parameters also...and that's double work. And
I need 3 programs. xdsconv, f2mtz and cad.



2015-10-19 12:00 GMT-05:00 Murpholino Peligro <murpholinox at gmail.com>:

> 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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