<div dir="ltr">Hi,<div><br></div><div>It took me a bit to figure it out, but the intensity lines you quote in the database listed are powder lines and are multiplicity weighted. If you take that into account, the calculated values have a better correspondence to the table listed, but are still not perfect which likely has to do with Pavel's suggestions as well as with the fact that bonding electrons breaking spherical symmetry have a contribution to the total. </div><div><br></div><div>Note that you can use this for reading in the cif file you attached earlier:</div><div><br></div><div><br></div><div><div>from __future__ import division</div><div>from cctbx import xray</div><div>from scitbx.array_family import flex</div><div>from libtbx import easy_pickle</div><div>from libtbx.str_utils import show_string</div><div>import sys, os</div><div>op = os.path</div><div><br></div><div>def run(args):</div><div> for f in args:</div><div> try:</div><div> xray_structures = xray.structure.from_cif(file_path=f)</div><div> except KeyboardInterrupt:</div><div> raise</div><div> except Exception, e:</div><div> print "Error extracting xray structure from file: %s:" % (</div><div> show_string(f))</div><div> print " ", str(e)</div><div> continue</div><div> basename, _ = op.splitext(op.basename(f))</div><div> for key, xs in xray_structures.items():</div><div> xs.show_summary()</div><div> r = basename</div><div> if key != r:</div><div> r += '_'+key</div><div> #easy_pickle.dump(file_name=r+'_xray_structure.pickle', obj=xs)</div><div> F = xs.structure_factors(d_min=1.5,algorithm='direct').f_calc()</div><div> I = F.as_intensity_array()</div><div> d = I.d_spacings().data()</div><div> m = I.multiplicities().data()</div><div> max_i = flex.max( I.data() )</div><div> for i,dd,mm in zip(I,d,m):</div><div> print i[0], i[1], dd,mm</div><div><br></div><div>if (__name__ == "__main__"):</div><div> import sys</div><div> run(args=sys.argv[1:])</div></div><div><br></div><div>resulting in </div><div><br></div><div><div>Number of scatterers: 1</div><div>At special positions: 1</div><div>Unit cell: (5.43094, 5.43094, 5.43094, 90, 90, 90)</div><div>Space group: F d -3 m :1 (No. 227)</div><div>(0, 2, 2) 4878.06695169 1.92012760466 12 100.0</div><div>(1, 1, 1) 3543.96579287 3.1355552483 8 48.4340187479</div><div>(1, 3, 1) 2144.13899149 1.63749032323 24 87.9093711801</div><div><br></div></div><div>these values are close to what Debye reported (contact me personally for the manuscript).</div><div><br></div><div>P</div><div><br></div><div><br></div><div> </div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 24, 2015 at 4:47 PM, Peter Zwart <span dir="ltr"><<a href="mailto:PHZwart@lbl.gov" target="_blank">PHZwart@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>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"><div><div class="h5"><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><br>
<br>
<div>On 8/24/15 15:01, Allan Lyckegaard
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div>
<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>
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<br></blockquote></div><br><br clear="all"><div><br></div></div></div>-- <br><div><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: <a href="tel:510%20289%209246" value="+15102899246" target="_blank">510 289 9246</a><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>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div style="font-size:small">-----------------------------------------------------------------<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/" style="color:rgb(17,85,204)" target="_blank">http://sastbx.als.lbl.gov</a></div><div style="font-size:small">BCSB: <a href="http://bcsb.als.lbl.gov/" style="color:rgb(17,85,204)" target="_blank">http://bcsb.als.lbl.gov</a><br></div><div style="font-size:small">PHENIX: <a href="http://www.phenix-online.org/" style="color:rgb(17,85,204)" target="_blank">http://www.phenix-online.org</a></div><div style="font-size:small">CAMERA: <a href="http://camera.lbl.gov/" target="_blank">http://camera.lbl.gov/</a></div><div style="font-size:small">-----------------------------------------------------------------</div></div></div></div></div>
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