[phenixbb] Find peaks and holes documentation

Nathaniel Echols nechols at lbl.gov
Thu Aug 22 09:01:23 PDT 2013

On Thu, Aug 22, 2013 at 8:43 AM, Morten Grøftehauge <
mortengroftehauge.work at gmail.com> wrote:

> So first the missing manual. If I google it I get this page
> http://www.phenix-online.org/documentation/find_peaks_holes.htm which is
> for the GUI. When I go back to the documentation
> http://www.phenix-online.org/documentation/phenix_documentation.html I
> can't find the link for it (which is also why I was using Google to find it
> in the first place). I also checked the source to see if the link was
> somehow misnamed.

The manual isn't "missing", I simply don't have time to cover every single
advanced feature in every section, and the behavior is fundamentally the
same as at least a dozen other programs (with respect to SHELX files,
anyway).  So far you're the first person to ask about command-line use.

Anyway, running it from the command line with default settings is not hard.
> phenix.find_peaks_holes model.pdb reflections.hkl
> but I run into this error message
> Sorry: Unresolved amplitude/intensity ambiguity:
> /path/path/path/reflections.hkl
>   SHELX reflection files may contain amplitudes or intensities.
>   Please append   =amplitudes
>              or   =hklf3
>              or   =intensities
>              or   =hklf4
>   to the file name argument or parameter to resolve the ambiguity.
>  and I don't how to do that. If I add .hklf3 at the end of the file name
> I get the same error. If I go reflections.hkl=hklf3 I just get a message
> that I need to supply a reflection file.
> What is the syntax?

phenix.find_peaks_holes model.pdb xray_data.file_name=reflections.hkl=hklf3

The same applies to most other programs which produce a similar error
message.  This is a little confusing, I agree.  I think it's mostly a
historical issue of the order in which various components of Phenix were
written.  Thinking about it a little bit, I think I can hack the code to
handle just "reflections.hkl=hklf3" as a special case.

I still find it inexplicable that in 2013 there are programs which are
still restricted to outputting a format which is fundamentally broken when
so many others are available.  We try to support any input format in
Phenix, but there are limits to how much time we can invest in compensating
for this.

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