<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Ilan,<div class=""><br class=""></div><div class=""> I'm a bit puzzled by what you are trying to do. It sounds like you are trying to make one map align with a PDB and then move several other maps that were aligned with that first map by the same transformation that aligned the first map.</div><div class=""><br class=""></div><div class=""> I think the simple approach is to eliminate steps 2 and 3.</div><div class=""><br class=""></div><div class=""> You start with your PDB and some reference map covering the PDB whose grid you will resample the maps on. Now fitmap your PDB to the first target map. Then move the reference grid to the same position as the fit PDB using the matrixcopy command to copy the PDB's position matrix to the grid map. Now just resample your first target and all the others on this reference grid and save them. If you then quit Chimera, restart, load the PDB and the new maps, the first target will be aligned with the PDB and the other targets will be moved by the same amount to align with the PDB.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/matrixcopy.html" class="">https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/matrixcopy.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 16, 2020, at 4:12 PM, Chemmama, Ilan <<a href="mailto:Ilan.Chemmama@ucsf.edu" class="">Ilan.Chemmama@ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Dear Developers,
<div class=""><br class="">
</div>
<div class="">I have a set of maps that I am trying to transform the following way:</div>
<div class=""><br class="">
</div>
<div class=""><u class="">i) Compute the transformation between a PDB and one of maps. </u></div>
<div class="">This is trivial using <i class="">fitmap</i> command. </div>
<div class=""><br class="">
</div>
<div class=""><u class="">ii) I would like to get the inverse transformation moving the PDB to its original position.</u></div>
<div class="">I have tried to play with matrixget and matrixes but without much success in access the the inverse transformation.</div>
<div class=""><br class="">
</div>
<div class=""><u class="">iii) Apply the inverse transformation to each of the map.</u></div>
<div class="">I assume you can easily do that with <i class="">move</i> passing the inverse matrix obtained above with a little for loop on model #. </div>
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</div>
<div class=""><u class="">iv) Save the rotated maps</u></div>
<div class="">This is trivial using <i class="">vop resample</i> and <i class="">
volume save.</i></div>
<div class=""><i class=""><br class="">
</i></div>
<div class=""><span style="font-style: normal;" class="">As you may see, I am struggling with step 2. Is there an easy way to access that matrix, get the inverse, and apply to a set of models. </span></div>
<div class=""><span style="font-style: normal;" class="">I have tried to find a solution in both Chimera (using runCommand) and ChimeraX (using run from core.commands) but to no avail. </span></div>
<div class=""><span style="font-style: normal;" class="">Any tips would be </span>appreciated here - </div>
<div class=""><br class="">
</div>
<div class="">Ilan</div>
</div>
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