<div dir="ltr">Hi Wolfram,<div><br></div><div>Does it work with the edited pdb file?<br></div><div><br></div>is_similar_symmetry is not called in model_vs_data directly, but via another function. There, tolerance parameters are 1e-2 for absolute cell lengths and angles.<div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 29, 2016 at 2:02 PM, wtempel <span dir="ltr">&lt;<a href="mailto:wtempel@gmail.com" target="_blank">wtempel@gmail.com</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">Hello Dorothee,<div>the &quot;mismatch&quot; flag did indeed lead me to edit the PDB&#39;s cell dimensions and model_vs_data runs.</div><div>With which tolerance parameters does model_vs_data call is_similar_symmetry? Tighter than the defaults listed in the documentation?</div><div>Regards,</div><div>Wolfram</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 29, 2016 at 4:43 PM, Dorothee Liebschner <span dir="ltr">&lt;<a href="mailto:dcliebschner@lbl.gov" target="_blank">dcliebschner@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">Hi Wolfram,<div><br></div><div><div style="font-size:12.8px">Yes, this is correct. The machinery used to read in the files uses is_similar_symmetry to check for symmetry mismatch.</div><div style="font-size:12.8px">As it is on a deeper level than model_vs_data, there is no keyword to override this, unfortunately.</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">In your example, did you try to edit your pdb file so that the unit cell dimensions match exactly?</div></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Best wishes,</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Dorothee</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 29, 2016 at 12:47 PM, wtempel <span dir="ltr">&lt;<a href="mailto:wtempel@gmail.com" target="_blank">wtempel@gmail.com</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><p style="margin:1.2em 0px!important">Hello,<br>phenix.model_vs_data_1.10.1-2155,<br>along with printing to stderr:<br><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248)">Sorry: Crystal symmetry mismatch between different files.</code></p>
<p style="margin:1.2em 0px!important">prints these, and only these, lines to stdout:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-radius:3px;display:inline;background-color:rgb(248,248,248);white-space:pre-wrap;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important">
x251682_scaled3.mtz (36.692, 53.798, 108.063, 90, 84.258, 90) P 1 21 1
readySet.pdb (36.69, 53.8, 108.06, 90, 84.26, 90) P 1 21 1

</code></pre>

<p style="margin:1.2em 0px!important">Is this related to <a href="http://cci.lbl.gov/cctbx_docs/cctbx/cctbx.crystal.html#cctbx.crystal.symmetry.is_similar_symmetry" target="_blank">this code</a>?<br>Can I force phenix.model_vs_data to omit this isomorphism check and “run” with the reflection dimensions?<br>Thank you.<br>Wolfram</p>
<div title="MDH:PGRpdj5IZWxsbyw8L2Rpdj48ZGl2PnBoZW5peC5tb2RlbF92c19kYXRhXzEuMTAuMS0yMTU1LDwv
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KT88L2Rpdj48ZGl2PkNhbiBJIGZvcmNlJm5ic3A7cGhlbml4Lm1vZGVsX3ZzX2RhdGEgdG8gb21p
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bWVuc2lvbnM/PGJyPjwvZGl2PjxkaXY+VGhhbmsgeW91LjwvZGl2PjxkaXY+V29sZnJhbTwvZGl2
PjxkaXY+PGJyPjwvZGl2PjxkaXY+PGJyPjwvZGl2PjxkaXY+PGJyPjwvZGl2PjxkaXY+PGJyPjwv
ZGl2PjxkaXY+PGJyPjwvZGl2PjxkaXY+PGJyPjwvZGl2Pg==" style="min-height:0;width:0;max-height:0;max-width:0;overflow:hidden;font-size:0em;padding:0;margin:0">​</div></div></div>
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