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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9">HeiHei!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9">I am refining a tetrahedral enzyme complex with Relion. For some reason I cannot get symmetry “T” to work. When I use D2 refinement gets to 3.2 Å
resolution with nice side chain density, but with T symmetry (and the reference map rotated such that one of the 3-folds is along z) I get huge angular (in)accuracies of 20-30 degrees, aka refinement fails.</span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9"> </span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9">I checked this webpage:</span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9"> </span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9"><a href="https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Conventions_%26_File_formats"><span style="color:#954F72">https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Conventions_%26_File_formats</span></a></span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9"> </span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9">and noticed “</span><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:black;background:#F9F9F9">3-fold axis on Z (deviating from Heymann et al!)</span><span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9">”.
This does not state where the 2-fold are expected. Furthermore, I cannot get the (misspelled) command mentioned below that table to work:</span><span style="color:black"><o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9">reline_refine --sym D7 --print_symmetry_ops</span><span style="color:black"><o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">And neither this command:<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Courier New";color:black;background:#F9F9F9">relion_refine --sym T --print_symmetry_ops</span><span style="color:black"><o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">which gives this error:<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">[hudel@aristotle]$ relion_refine --sym T --print_symmetry_ops</span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">The following errors were encountered upon command-line parsing:</span></span><span class="apple-converted-space"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"> </span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">ERROR: Argument --i not found or invalid argument</span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">ERROR: Argument --o not found or invalid argument</span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">ERROR:</span></span><span class="apple-converted-space"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"> </span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">Errors encountered on the command line (see above), exiting...</span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">File: /lsc/sources/relion/src/ml_optimiser.cpp line: 1286</span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span class="s1"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D">[hudel@aristotle]$</span></span><span class="apple-converted-space"><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"> </span></span><span style="font-size:13.5pt;font-family:Menlo;color:#02FF0D"><o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">Does anyone know how I should reorient my reference map (and mask) for full T (12x) symmetry refinement instead of D2 (4x)? For example the chimera or dynamo commands? Or, better yet, is there a secret T setting in Relion that allows
the 2-folds to remain on the principal axes (and a 3-fold on 1,1,1)? Checking the source code I found Th and Td, but these have extra (achiral) symmetry elements.
<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">Thanks, Hudel<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">--<o:p></o:p></span></p>
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<span style="color:black">Prof. Hartmut Luecke<o:p></o:p></span></p>
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<span style="color:black">Structural Biology and Drug Discovery<o:p></o:p></span></p>
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<span style="color:black">Nordic Centre for Molecular Medicine<o:p></o:p></span></p>
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<span style="color:black">Dept. of Medical Biochemistry<o:p></o:p></span></p>
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<span style="color:black">Gaustadalléen 21<o:p></o:p></span></p>
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<span style="color:black">0318 Oslo<o:p></o:p></span></p>
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<span style="color:black">Norway<o:p></o:p></span></p>
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