[phenixbb] Find peaks and holes documentation

Morten Grøftehauge mortengroftehauge.work at gmail.com
Thu Aug 22 08:43:13 PDT 2013


I wanted to try phenix.find_peaks_holes with anomalous structure factors
from XPREP but I ran into a few problems. And then I tried to fix them by
reading the manual and that was really hard too.

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.

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:
  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?


Morten K Grøftehauge, PhD
Pohl Group
Durham University
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