[phenixbb] Find peaks and holes documentation

Nathaniel Echols nechols at lbl.gov
Thu Aug 22 09:02:31 PDT 2013

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:



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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