<div dir="ltr"><div>Hi,</div><div><br></div><div>There are two standard space group settings for F d -3 m (namely 1 and 2) and I am not sure what the literature uses. </div><div>It is a puzzle indeed, in one setting (2,2,0) is absent, in another it isn't. I guess the difference is space group settings, but the choice between setting 1 and 2 still doesn't reproduce the table you send, which by chance isn't in the paper listed in the link you send.<br></div><div><br></div><div>P</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><div><div><br></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 24 August 2015 at 15:55, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@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 text="#000000" bgcolor="#FFFFFF">
Hi Allan,<br>
<br>
I'm not entirely sure why the difference between observed
(experimentally measured) and calculated (using your script below)
amplitudes of structure factors surprises you..<br>
<br>
Also:<br>
<br>
- your script computes structure factors and prints out amplitudes
(not intensities);<br>
- you do not set the B-factor. By default scatterer object is
constructed with u_iso=0.<br>
<br>
Pavel<div><div class="h5"><br>
<br>
<div>On 8/24/15 15:01, Allan Lyckegaard
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">Dear CCTBX-list
<div><br>
</div>
<div>I am trying to reproduce the (scaled) intensities for Si
reported here: <a href="http://rruff.geo.arizona.edu/AMS/xtal_data/DIFfiles/15285.txt" target="_blank">http://rruff.geo.arizona.edu/AMS/xtal_data/DIFfiles/15285.txt</a>
based on this information: <a href="http://rruff.geo.arizona.edu/AMS/CIF_text_files/15285_cif.txt" target="_blank">http://rruff.geo.arizona.edu/AMS/CIF_text_files/15285_cif.txt</a></div>
<div><br>
</div>
<div>I am using CCTBX in Python:</div>
<div><br>
</div>
<div>
<p style="margin:0px">from cctbx.array_family import flex </p>
<p style="margin:0px">from cctbx import sgtbx, crystal,
miller, xray</p>
<p style="margin:0px">sgnum = 227</p>
<p style="margin:0px">sg =
sgtbx.space_group_info(sgnum).group()</p>
<p style="margin:0px">latticepar = [5.43070, 5.43070, 5.43070,
90, 90, 90]</p>
<p style="margin:0px">dmin = 1.0</p>
<p style="margin:0px">atompos = [['Si',(0.0, 0.0, 0.0)]]</p>
<p style="margin:0px">scatterers = flex.xray_scatterer()</p>
<p style="margin:0px">scatterers.append(xray.scatterer(label=atompos[0][0],
site=atompos[0][1]))</p>
<p style="margin:0px">pg = sg.build_derived_point_group()</p>
<p style="margin:0px">sym =
crystal.symmetry(space_group=sg,unit_cell=latticepar)</p>
<p style="margin:0px">sps =
crystal.special_position_settings(crystal_symmetry=sym)</p>
<p style="margin:0px">structure =
xray.structure(special_position_settings=sps,scatterers=scatterers)</p>
<p style="margin:0px">F =
structure.structure_factors(d_min=dmin,algorithm='direct').f_calc()</p>
<p style="margin:0px">list(F.amplitudes())</p>
<p style="margin:0px"><br>
</p>
<p style="margin:0px">This gives:</p>
<p style="margin:0px">[((0, 2, 2), 0.0),</p>
<p style="margin:0px"> ((0, 4, 0), 120.21765812638594),</p>
<p style="margin:0px"> ((1, 1, 1), 84.18849550806966),</p>
<p style="margin:0px"> ((1, 3, 1), 65.48371727205928),</p>
<p style="margin:0px"> ((1, 3, 3), 57.45438308324155),</p>
<p style="margin:0px"> ((1, 5, 1), 51.48759686950681),</p>
<p style="margin:0px"> ((2, 2, 2), 128.54540698861973),</p>
<p style="margin:0px"> ((2, 4, 2), 0.0),</p>
<p style="margin:0px"> ((3, 3, 3), 51.48759686950681)]</p>
</div>
<div><br>
</div>
<div>How come CCTBX give an amplitude of 0.0 for (0,2,2) and
(2,4,2)? The measured intensities in the DIFfile above does
not show this. Am I missing something?</div>
<div><br>
</div>
<div>Cheers,</div>
<div>/Allan</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div></div><pre>_______________________________________________
cctbxbb mailing list
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a>
</pre>
</blockquote>
<br>
</div>
<br>_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>-----------------------------------------------------------------<br>P.H. Zwart<br>Staff Scientist<br>Berkeley Center for Structural Biology, Science lead<br>Lawrence Berkeley National Laboratories<br>1 Cyclotron Road, Berkeley, CA-94703, USA<br>Cell: 510 289 9246<br>SASTBX: <a href="http://sastbx.als.lbl.gov" target="_blank">http://sastbx.als.lbl.gov</a></div><div>BCSB: <a href="http://bcsb.als.lbl.gov" target="_blank">http://bcsb.als.lbl.gov</a><br></div><div>PHENIX: <a href="http://www.phenix-online.org" target="_blank">http://www.phenix-online.org</a></div><div>CAMERA: <a href="http://camera.lbl.gov/" target="_blank">http://camera.lbl.gov/</a></div><div>-----------------------------------------------------------------</div></div></div></div></div>
</div>