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<p class="MsoNormal"><span lang="EN-US">Good day<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use
a citation for sure when I publish using your software.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the
number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of
each residue and the different number comes from the difference residue number at the end of the chains.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all
atoms all together.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">In addition a small question which I guess wont be possible – is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthias<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-NZ"><img width="381" height="499" id="Picture_x0020_1" src="cid:image001.png@01CFDE66.FDAB5BD0"></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">with these parameters:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> chain pairing: bb<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> Needleman-Wunsch using BLOSUM-62<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ss fraction: 0.3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> gap open (HH/SS/other) 18/18/6, extend 1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> iteration cutoff: 2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">RMSD between 191 atom pairs is 0.506 angstroms<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">with these parameters:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> chain pairing: bb<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> Needleman-Wunsch using BLOSUM-62<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ss fraction: 0.3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> gap open (HH/SS/other) 18/18/6, extend 1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> iteration cutoff: 2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">RMSD between 188 atom pairs is 0.551 angstroms<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">with these parameters:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> chain pairing: bb<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> Needleman-Wunsch using BLOSUM-62<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ss fraction: 0.3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> gap open (HH/SS/other) 18/18/6, extend 1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> iteration cutoff: 2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">RMSD between 193 atom pairs is 0.336 angstroms<o:p></o:p></span></p>
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