<div dir="ltr">Thank you for the quick reply. <div style><br></div><div style>I am quite okay with not everything being documented from top to bottom. I found it weird that the GUI documentation wasn't linked up in the documentation index.</div>
<div style><br></div><div style>And I think an easier hack would be to write in the error message:</div><div style><span style="font-family:'courier new',monospace;font-size:13px">Example:</span></div><div style><span style="font-family:'courier new',monospace;font-size:13px">xray_data.file_name=</span><font face="courier new, monospace">reflections.hkl=hklf3</font><br>
</div><div style><font face="arial, helvetica, sans-serif"><br></font></div><div style><font face="arial, helvetica, sans-serif">Example syntax is the simplest way to explain anything.</font></div><div style><font face="arial, helvetica, sans-serif"><br>
</font></div><div style><font face="arial, helvetica, sans-serif">But I just tried it and I get </font></div><div style><font face="arial, helvetica, sans-serif">Sorry: Couldn't find the file reflections.hkl=hklf3<br>
</font></div><div style><font face="arial, helvetica, sans-serif"><br></font></div><div style>/mo</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 22 August 2013 17:02, 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">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:<div>
<br></div><div>r_free_flags.file_name=flags.mtz</div><div><br></div><div>-Nat</div></div><div class="HOEnZb"><div class="h5"><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>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><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><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). So far you're the first person to ask about command-line use.</div>
<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><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. 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><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>
</div></div><br>_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Morten K Grøftehauge, PhD <div>Pohl Group</div><div>Durham University</div>
</div>