<div dir="ltr">Hi Patrick, <div><br></div><div>The quick and easy way of doing this would be to use Rob Nicholls' ProSMART in CCP4. It does a local structure alignment and gives you a value for the superposition of main chain atoms. </div>
<div>I don't know of any tool in Phenix that does this. </div><div><br></div><div>Cheers, </div><div>Morten </div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 8 July 2014 14:56, MARTYN SYMMONS <span dir="ltr"><<a href="mailto:martainn_oshiomains@btinternet.com" target="_blank">martainn_oshiomains@btinternet.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">That's a reasonable approach and I think that it is similar to the one used by FATCAT - which I notice is the basis for structural comparison at the RCSB site.<br>
Motivation and some results in the paper ( <a href="http://www.ncbi.nlm.nih.gov/pubmed/14534198" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/14534198</a>)<br>
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It's not clear to me, though, how to fairly compare the resulting RMSD of fragments with twists between. If I introduce an arbitrary number of twists then I can improve the rmsd artificially. In sequence matching there is a penalty for introducing a gap and that is scaled compared with the amino acid substitution scoring to split the match into a 'reasonable' number of sub-alignments. Obviously in 3D case there should also be a penalty for introducing a split in the structure to do a twist re-orientation - but how to quantify it compared with RMSD and get a global score?<br>
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Seems to me better would be to express the whole problem in torsional space - so the twists would be large displacements while the matched sections should have close fit in torsional angles. And a global score could be calculated. Someone must have tried this?<br>
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All the best<br>
Martyn<br>
Cambridge<br>
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