[phenixbb] Find peaks and holes documentation

Morten Grøftehauge mortengroftehauge.work at gmail.com
Thu Aug 22 09:26:57 PDT 2013

Thank you for the quick reply.

I am quite okay with not everything being documented from top to bottom. I
found it weird that the GUI documentation wasn't linked up in the
documentation index.

And I think an easier hack would be to write in the error message:

Example syntax is the simplest way to explain anything.

But I just tried it and I get
Sorry: Couldn't find the file reflections.hkl=hklf3


On 22 August 2013 17:02, Nathaniel Echols <nechols at lbl.gov> wrote:

> PS. You will still need R-free flags to use this program.  I have no idea
> if the XPREP output includes these, or whether the =hklf3 hack will still
> allow them to be detected, but if not, you will need to specify those as a
> separate file:
> r_free_flags.file_name=flags.mtz
> -Nat
> On Thu, Aug 22, 2013 at 9:01 AM, Nathaniel Echols <nechols at lbl.gov> wrote:
>> 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.
>> -Nat
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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