<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Dear Hong,<div class="">I broke this down into (A) showing Dali 3D superposition, and (B) showing sequence alignment and RMSD values.</div><div class=""><br class=""><div class=""><div class="">(A) showing Dali 3D superposition. Unfortunately the Dali Server <<a href="http://ekhidna2.biocenter.helsinki.fi/dali/" class="">http://ekhidna2.biocenter.helsinki.fi/dali/</a>> does not give anything as convenient as a PDB file!</div><div class=""><br class=""></div><div class="">However, you can use the transformation matrix provided by the Dali Server with the ChimeraX "view matrix" command to superimpose the structures. You would not use matchmaker, because Dali already calculated the superposition. You simply want to apply the Dali superposition.</div><div class=""><br class=""></div><div class="">Details:</div><div class=""><br class=""></div><div class="">(1) I tried the Dali Server with first structure 2gbpA and second structure 2fw0A. Then I got a results page that looks like this:</div><div class=""><img apple-inline="yes" id="5189E491-F94F-4F53-87B8-A81E8F57FA4B" width="338" height="134" src="cid:C1FF6C45-930F-47CE-BC54-08926B95238A@gateway.sonic.net" class=""></div><div class="">(2) then I clicked the "Parseable (txt)" link and I got a page that looks like this. (You could also save it as a text file from your web browser).</div><div class=""><img apple-inline="yes" id="58C0E960-D7EF-48BE-BF15-12DEE252579F" width="581" height="157" src="cid:4BBD9B42-0373-4B61-A156-5485A00E4CB4@gateway.sonic.net" class=""></div><div class=""><br class=""></div><div class="">(3) then I reformatted those 12 numbers in the matrix to use in the ChimeraX "view matrix" command. In ChimeraX, I opened 2gbp (model #1) and 2fw0 (model #2) and then used the following command, which should all be one line even though the email may display as multiple lines:</div><div class=""><br class=""></div><div class="">view matrix mod #2,-0.464817,-0.320176,0.825489,65.924568,-0.856265,0.399781,-0.327087,21.951881,-0.225289,-0.858873,-0.459981,18.394049</div><div class=""><br class=""></div><div class="">See help</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix</a>></div><div class=""><br class=""></div><div class="">(B) Showing sequence alignment and RMSD values.</div><div class=""><br class=""></div><div class=""> I couldn't figure out how to get a sequence alignment file that can be used as ChimeraX input from the Dali server either! But it sounds like you were able to do it. If so, you can just open the file in ChimeraX and show the RMSD header and use it for coloring:</div><div class=""><br class=""></div><div class="">sequence header rmsd show</div><div class="">color byattribute seq_rmsd #2<br class=""></div><div class=""><br class=""></div><div class="">You need to show the RMSD header in order to be able to color by the seq_rmsd header values. </div><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#header" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#header</a>><div class=""><br class=""></div><div class="">You can use different coloring if you like:<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute</a>><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options</a>></div><div class=""><br class=""></div><div class="">Since I couldn't figure out how to get the sequence alignment from Dali, I used ChimeraX for that part too. If it is just a pairwise comparison, actually you can use ChimeraX matchmaker to show the sequence alignment withRMSD header:</div><div class=""><br class=""></div><div class="">mm #2 to #1 show true</div><div class=""><br class=""></div><div class="">But *after* that matchmaker command, you would then need to use the "view matrix" command from part (A) above, to apply the Dali superposition instead of simply using the matchmaker superposition, if the Dali one is what you want. Then you can color by the seq_rmsd attribute as shown above.</div><div class=""><br class=""></div><div class="">If it is >2 structures, then you have to resort to other methods of getting the sequence alignment. One way is to open all of the structures in ChimeraX, then use the "seq align" command to use a web service to make a multiple sequence alignment. This command is a recent feature, so it is not in the version 1.3 release -- you would need to get a new daily build to use it. Example if you want sequence alignment of #1 chain A, #2 chain A, #3 chain B:</div><div class=""><br class=""></div><div class="">seq align #1/A #2/A #3/B</div><div class="">sequence header rmsd show</div><div class=""><br class=""></div><div class="">See "seq align" help:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""></div><blockquote type="cite" class="">On Apr 29, 2022, at 8:14 PM, HONG ZHAN via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Dear all, <br class="">I am trying to align molecules based on Dali server output. However, I can’t download the superposition results from the Dali server webpage (or anyone know?), but I can generate an alignment file with 2D structural alignment from the Dali server. Is there a way to use matchmaker to superpose molecules based on output alignment from Dali server? How to run structure conservation calculation to color the molecule? If I just give Dali’s alignment file, it still calculate conservation based on sequence not structure. <br class="">Best,<br class="">Hong<br class=""></blockquote><br class=""></div></div></div></body></html>