<div dir="ltr">Hi James, thanks.  I looked at random image 15 and after trying a bunch of stuff it indexes fine if I use indexing.method=fft3d.  The default for stills processing is fft1d, so I find this super interesting.<div><br></div><div>For what it&#39;s worth, I pretty much never process stills without a target cell.  I generated ~30 random images using your script and indexed them, then I got the unit cells with &quot;dials.show *refined*.json | grep cell&quot;.  They were all about the same.  So I re-indexed random image 15 using fft1d but I also specified known_symmetry.cell=50,60,70,<wbr>90,90,90 and it indexed fine.</div><div><br></div><div>So, either <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">indexing.method=fft3d or <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">known_symmetry.cell=50,60,<wbr>70,90,90,90 is sufficient to index random image 15.  Certainly for experimental data I would recommend using known_symmetry as the results are always better.  However, I&#39;d like to look deeper at fft1d vs fft3d at some point.</span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Cc&#39;ing dials-support.</span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></span></div><div>Thanks!</div><div>-Aaron</div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Feb 2, 2018 at 1:35 PM, James Holton <span dir="ltr">&lt;<a href="mailto:jmholton@lbl.gov" target="_blank">jmholton@lbl.gov</a>&gt;</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><div><div><div><div><div><div><div>While testing the new simTBX diffraction image simulator Aaron and I found that some rather beautiful-looking images still won&#39;t index.  Subsequently, I followed up with mosflm, which does succeed in these cases, even without prior knowledge of the cell or space group.<br><br></div>I have now run this 1000 times, varying only the crystal orientation, and found 171 cases of dials.stills_process failing to index the simulated image whereas mosflm had no trouble, and 5 cases where mosflm failed and dials.stills_process succeeded.  There were no overlapping cases where both programs failed. <br><br></div>I have tarballed up the relevant files here:<br><a href="http://bl831.als.lbl.gov/~jamesh/bugreports/dials_index_020218.tgz" target="_blank">http://bl831.als.lbl.gov/~jame<wbr>sh/bugreports/dials_index_0202<wbr>18.tgz</a><br><br></div>The tarball contains a &quot;<a href="http://runme.com" target="_blank">runme.com</a>&quot; shell script for reproducing these results, and also the tst_nanoBragg_forindex.py jiffy for making a test image given a provided random-number seed.  For example:<br><br></div>libtbx.python ./tst_nanoBragg_forindex.py random 15<br><br></div>will create a file called noiseimage_001.cbf that dials.stills_process cannot index (at least in my hands).  For those of you who don&#39;t have mosflm installed, the tarball incluses a copy, and the &quot;<a href="http://autoindex.com" target="_blank">autoindex.com</a>&quot; script should run on any linux system.<br><br></div>Any ideas as to why there is this discrepancy?  Feels like an opportunity for a non-trivial improvement.<br><br></div>Something to ponder over the weekend, I suppose.  Note that I recently checked in a few bug fixes to simTBX, but this 
analysis is unaffected by them, so you shouldn&#39;t have to update your 
build to reproduce this.<br><br></div>Cheers,<br><div><br>-James Holton<br></div><div>MAD Scientist<br><br></div><div><br></div></div>
<br>______________________________<wbr>_________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailm<wbr>an/listinfo/cctbxbb</a><br>
<br></blockquote></div><br></div></div>