<div dir="ltr">Dear Sergei,<div><br></div><div>If you use Chimera, try to manually align the two maps. Then, open Fit in Map (Tools/Volume Data/Fit in Map), if you press fit in Map, the alignment will take place. You can see the parameters by opening Favourites/Reply Log. The alignment parameter will look like this:</div><div><br></div><div><div>Fit map A.map in map B.map using 608907 points</div><div> correlation = 0.8745, correlation about mean = 0.3838, overlap = 2.159e+07</div><div> steps = 80, shift = 13.8, angle = 3.88 degrees</div><div>Position of A.map (#1) relative to B.map (#0) coordinates:</div><div> Matrix rotation and translation</div><div> -0.31907565 -0.94727261 0.02941662 968.10738925</div><div> 0.94766668 -0.31925750 -0.00158170 561.43029040</div><div> 0.01088978 0.02737247 0.99956599 -7.05144295</div><div> Axis 0.01527722 0.00977540 0.99983551</div><div> Axis point 282.50181304 628.39781990 0.00000000</div><div> Rotation angle (degrees) 108.62565060</div><div> Shift along axis 13.22791470</div></div><div><br></div><div>The other way is to open IDLE in Chimera (Tools/General Control).</div><div><br></div><div>Type:</div><div>om = chimera.openModels</div><div>mlist = om.list()</div><div>m = mlist[0] # First map. m = mlist[1] will get you the 2nd map</div><div>print m.openState.xform # 3x3 rotation matrix, ast column is translation</div><div><br></div><div><div>-0.841777 -0.53957 -0.0165966 1273.53</div><div>-0.538462 0.841438 -0.0451738 427.043</div><div>0.0383394 -0.0290897 -0.998841 1228.6</div></div><div><br></div><div>For un-translated & rotated map, your output will be like:</div><div><div>1 0 0 0</div><div>0 1 0 0</div><div>0 0 1 0</div></div><div><br></div><div>Look at more detail in here <a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html</a> to understand Chimera's xform matrix.</div><div><br></div><div>Best,</div><div>Huy</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 29, 2015 at 9:10 AM, Penczek, Pawel A <span dir="ltr"><<a href="mailto:Pawel.A.Penczek@uth.tmc.edu" target="_blank">Pawel.A.Penczek@uth.tmc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Sergej,<br>
<br>
Chimera offers reach environment for manipulation and alignment of EM maps. To transfer the results<br>
to human-friendly format and to manipulate them further in SPARX you can use simple python<br>
scripts described here:<br>
<a href="http://sparx-em.org/sparxwiki/align_chimera" rel="noreferrer" target="_blank">http://sparx-em.org/sparxwiki/align_chimera</a><br>
<br>
They read Chimera orientation matrices and, if needed, apply transformations directly to EM maps.<br>
<br>
Regards,<br>
-<br>
Pawel Penczek<br>
<a href="mailto:pawel.a.penczek@uth.tmc.edu">pawel.a.penczek@uth.tmc.edu</a><br>
<span class=""><br>
<br>
<br>
<br>
> On Jul 29, 2015, at 8:05 AM, Sergej Masich <<a href="mailto:Sergej.Masich@ki.se">Sergej.Masich@ki.se</a>> wrote:<br>
><br>
> Dear colleagues,<br>
><br>
> I am looking for a program(s) that would allow me to align manually two density maps. We have reconstructed several particles that may have a common origin and we are trying to trace common features in these particles. We have software that presumably may help us but it requires pre-aligned densities.<br>
><br>
> I checked Chimera that allows storing rotational and translational parameters for individual maps in Python scripts for saved session. However, I cannot find any definition of these parameters. Moreover, I have not found any routine in Chimera to apply these parameters to reorient tomographic maps.<br>
><br>
> Can you advise a program/set of programs that would allow me to (1) align two tomographic maps under visual control; (2) store corresponding rotational and translational parameters; and (3) use these parameters to obtain aligned densities?<br>
><br>
> Any advice is appreciated. Thank you in advance.<br>
><br>
> Sergej Masich<br>
> =============================<br>
> Dr. Sergej Masich<br>
> Dept. of Cell and Molecular Biology<br>
> Karolinska Institutet<br>
> Box 285<br>
> 171 77 Stockholm, Sweden<br>
> tel: (+)46 - 8 - 524 873 61<br>
> mobile: (+)46 - 736 - 833 693<br>
> e-mail: <a href="mailto:Sergej.Masich@ki.se">Sergej.Masich@ki.se</a><br>
><br>
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