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<p>Hi Hudel,</p>
<p>Reconstructions of higher symmetries can get lost unless the
initial reference is good and aligned, since the symmetrization
will cause a strong "inertia" or reference bias. You therefore
need to make sure your initial reference is both good and aligned.
<br>
</p>
<p>To align a reference to T-sym, open it and any output from a
relion-run where T-sym was used. Now, in chimera, rotate the
reference you want to use so that it very closely aligns with the
T-sym output. To be clear; the T-sym output does not need to be
good or high-res, you just need to see which symmetry is enforced
around which axis. Having aligned them, use
Favourites->commandline and run <br>
</p>
<p>vop resample #x onGrid #y <br>
</p>
<p>where #x is the volume number of your reference and #y is that of
your T-sym output. Save the new volume and use as a T-sym
reference. Note also that with higher symmetries, it is
recommended that you increase the orientation-sampling. This is
because there's a smaller number of unique views to search, making
it both computationally tractable and better for results to
subdivide those views into smaller groups.<br>
</p>
<p>To comment on your other questions; there is no way to modify the
symmetry definitions in RELION by flags, but you can alter the
symmetry ops in the source code if you want. You can print the
symmetry ops using the flags you show, but there are certain flags
you must always specify to make relion get far enough to print
them, like --i and --o. In this case it doesn't really make sense
to demand those flags, but you can just put some dummy filenames
there. <br>
</p>
<p>/Björn<br>
</p>
<br>
<div class="moz-cite-prefix">On 2018-03-31 13:14, Luecke, Hartmut
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:13BAB651-FD24-4B70-8491-AFB58F9C6D75@ncmm.uio.no">
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<div class="WordSection1">
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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"
moz-do-not-send="true"><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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">And neither this command:<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">which gives this error:<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="p1"
style="margin:0in;margin-bottom:.0001pt;background:black;font-variant-caps:
normal;orphans: auto;text-align:start;widows:
auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width:
0px;background-position:initial
initial;background-repeat:initial initial;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<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>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">Thanks, Hudel<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">--<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">Prof. Hartmut Luecke<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">Structural Biology and Drug
Discovery<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">Nordic Centre for Molecular Medicine<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">Dept. of Medical Biochemistry<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">Gaustadalléen 21<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">0318 Oslo<o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans:
auto;text-align:start;widows: auto;-webkit-text-size-adjust:
auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black">Norway<o:p></o:p></span></p>
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