<div dir="ltr">PS. You will still need R-free flags to use this program. 狢 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:<div>
<br></div><div>r_free_flags.file_name=flags.mtz</div><div><br></div><div style>-Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Aug 22, 2013 at 9:01 AM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="im">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><div class="gmail_quote"><div class="im"><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>©ðhich 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>狢 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><div>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). 䒷o far you're the first person to ask about command-line use.</div>
<div class="im">
<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">� � � � � � 䰄r � =hklf3</font></div>
<div><font face="courier new, monospace">� � � � � � 䰄r � =intensities</font></div><div><font face="courier new, monospace">� � � � � � 䰄r � =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>蟵nd 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><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>The same applies to most other programs which produce a similar error message. �This is a little confusing, I agree. 狢 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><br></div><div>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><br></div><div>-Nat</div></div></div></div>
</blockquote></div><br></div>