Hi,

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: /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?

Cheers,

Morten

--
Morten K Grøftehauge, PhD

Pohl Group

Durham University