<div dir="ltr"><div class="gmail_extra">On Thu, Aug 22, 2013 at 8:43 AM, Morten Grøftehauge <span dir="ltr"><<a href="mailto:mortengroftehauge.work@gmail.com" target="_blank">mortengroftehauge.work@gmail.com</a>></span> wrote:<br>
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div>So first the missing manual. If I google it I get this page <a href="http://www.phenix-online.org/documentation/find_peaks_holes.htm" target="_blank">http://www.phenix-online.org/documentation/find_peaks_holes.htm</a> which is for the GUI. When I go back to the documentation <a href="http://www.phenix-online.org/documentation/phenix_documentation.html" target="_blank">http://www.phenix-online.org/documentation/phenix_documentation.html</a> 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.</div>
</div></blockquote><div><br></div><div style>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.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div>Anyway, running it from the command line with default settings is not hard.</div>
<div><br></div><div><font face="courier new, monospace">phenix.find_peaks_holes model.pdb reflections.hkl</font></div>
<div><br></div><div>but I run into this error message </div><div><br></div><div><div><font face="courier new, monospace">Sorry: Unresolved amplitude/intensity ambiguity: /path/path/path/reflections.hkl</font></div>
<div><font face="courier new, monospace"> SHELX reflection files may contain amplitudes or intensities.</font></div><div><font face="courier new, monospace"> Please append =amplitudes</font></div><div><font face="courier new, monospace"> or =hklf3</font></div>
<div><font face="courier new, monospace"> or =intensities</font></div><div><font face="courier new, monospace"> or =hklf4</font></div><div><font face="courier new, monospace"> to the file name argument or parameter to resolve the ambiguity.</font></div>
<div><br></div></div><div> and I don't how to do that. If I add <font face="courier new, monospace">.hklf3</font> at the end of the file name I get the same error. If I go <font face="courier new, monospace">reflections.hkl=hklf3</font> I just get a message that I need to supply a reflection file. </div>
<div>What is the syntax?</div></div></blockquote><div><br></div><div>p<span style="font-family:'courier new',monospace">henix.find_peaks_holes model.pdb xray_data.file_name=reflections.hkl=hklf3</span></div><div>
<span style="font-family:'courier new',monospace"><br></span></div><div style>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.</div>
<div style><br></div><div style>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.</div>
<div style><br></div><div style>-Nat</div></div></div></div>