[phenixbb] About the phenix.mtz_as_cif

Oleg Sobolev osobolev at lbl.gov
Thu Aug 25 14:34:20 PDT 2016

Dear Huawang,

The tool will automatically recognize most of the labels from Phenix and
and convert them to appropriate labels for mmCIF format. If some labels are
not recognized,
or another mmCIF labels are needed for them, one may use mtz_labels and
cif_labels parameters to provide pairs of mtz and cif labels. Note that
cif_labels must comply with mmCIF format. Number of mtz_labels should be
to number of cif_labels.

In command-line, for example:
phenix.mtz_as_cif data.mtz output_file=custom.cif mtz_labels="FOBS SIGFOBS"
      cif_labels="_refln.custom1 _refln.custom2"
Or you can put these instructions in .eff file.
Basically, mtz_labels and cif_labels are just white-space separated lists.
In this example FOBS will become _refln.custom1 and SIGFOBS will become

To find out what labels you have in mtz file you may use phenix.mtz.dump

Also note, that this functionality is available in GUI: Utilities-> Convert
MTZ to mmCIF.

Hope this helps,
Best regards,
Oleg Sobolev.

On Thu, Aug 25, 2016 at 11:58 AM, Huanwang Yang <hyang at rcsb.rutgers.edu>

> Dear Oleg,
> Thank you so much for your help.
> In the parameter file, what should I give to the labels below
>   mtz_labels = None
>   cif_labels = None
> Could you provide an simple example for them? Thanks a lot.
> Best,
> Huawang
> On 08/25/2016 01:49 PM, Oleg Sobolev wrote:
> Please find some about phenix.mtz_as_cif usage below. In the next nightly
> build it will be displayed if you run the tool without arguments. Please
> let me know if you need additional information.
> Best regards,
> Oleg Sobolev.
> phenix.mtz_as_cif: Convert mtz to CIF format.
> Usage: phenix.mtz_as_cif data.mtz [params.eff] [options ...]
> Usage examples:
>   phenix.mtz_as_cif data.mtz
> ------------------------------------------------------------
> -------------------
> mtz_as_cif {
>   mtz_file = None
>   output_file = None
>   mtz_labels = None
>   cif_labels = None
> }
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160825/a713bd19/attachment.htm>

More information about the phenixbb mailing list