<div dir="ltr">Dear Jan,<div><br></div><div style>this is an interesting problem and there are no perfect solutions. 狢'm not currently a cctbx user so I can't say whether such an algorithm is implemented but I done some work on this myself and can maybe point you in the direction of some approaches you could take.</div>
<div style><br></div><div style>* Sorted distances (possibly the simplest approach)</div><div style><br></div><div style>1) Calculate all r_ij distances from all the atoms in your unit cell to all neighbours within a cutoff.</div>
<div style>2) Sort the list of distances.</div><div style>3) To get the 'difference' between the two structures calculate the rms of the differences in distances between the two lists.</div><div style><br></div><div style>
Generally this approach works well although it can give false positives (by virtue of the fact that it's throwing away a lot of information)</div><div style><br></div><div style>* Histogram radial distribution comparison (real space)</div>
<div style><br></div><div style>See:�<a href="http://www.ncbi.nlm.nih.gov/pubmed/20720316">http://www.ncbi.nlm.nih.gov/pubmed/20720316</a> for details.</div><div style><br></div><div style>Basically calculate the radial distribution histogram for each species pair and then use some method to calculate the difference between the histograms (e.g. rms differences, cosine distance, etc.)</div>
<div style><br></div><div style>* Frequency space comparison</div><div style><br></div><div style>See�<a href="http://arxiv.org/abs/0805.1418">http://arxiv.org/abs/0805.1418</a> for details.</div><div style><br></div><div style>
Similar to calculating the r-factor although in this paper they use a more sophisticated approach that I don't fully understand.</div><div style><br></div><div style>* Finding ideal transformation between structures</div>
<div style><br></div><div style>Hundt's approach (CMPZ):</div><div style><a href="http://scripts.iucr.org/cgi-bin/paper?S0021889805032450">http://scripts.iucr.org/cgi-bin/paper?S0021889805032450</a><br></div><div style>
<br></div><div style>Lonie's approach (XtalComp):</div><div style><a href="http://www.sciencedirect.com/science/article/pii/S0010465511003699">http://www.sciencedirect.com/science/article/pii/S0010465511003699</a></div>
<div style>for details and</div><div style><a href="http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html">http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html</a></div><div style>to try the algorithm for yourself.</div>
<div style><br></div><div style>Basically the idea is to find the more ideal transformation to take you from one crystal structure to another. 硓rom the transformation you can then pull out one number to get a difference or use it to map from one system to another.</div>
<div style><br></div><div style>I think I'll stop there but I'd be curious to hear about what you find and how you get on.</div><div style><br></div><div style>All the best,</div><div style>-Martin</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 4 March 2013 12:06, Jan Marten Simons <span dir="ltr"><<a href="mailto:marten@xtal.rwth-aachen.de" target="_blank">marten@xtal.rwth-aachen.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I think I've seen some code in cctbx which tries to put the similarity of two<br>
crystal structures into a number. Am I right on this?<br>
<br>
I want to have something similar:<br>
<br>
I'm interested in comparing the direct space atomic distances of two<br>
structures sharing the same unit cell parameters and space group and<br>
scatterers but different atomic coordinates for those. Now I'd like to have a<br>
mapping where I could compare the bond lengths between all scatterers which<br>
should eliminate any movements which might also be due to a shift in the<br>
origin of a P 1 cell. Also I'd like to have a value for mean, minimal and<br>
maximal displacements.<br>
The purpose of this is to check how good a structure approximation matches a<br>
reference structure.<br>
<br>
How would you suggest to take on this task? Or is there even some code related<br>
to this?<br>
<br>
Thanks in advance,<br>
<br>
Jan<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><span style="border-collapse:collapse;color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">Martin Uhrin � � � � � � � � � � � � � � � � � � � � � � � � �Tel: +44 207 679 3466<br>
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