[3dem] Manual alignment of density maps

[Huy Bui]

Dear Sergei,

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:

Fit map A.map in map B.map using 608907 points
  correlation = 0.8745, correlation about mean = 0.3838, overlap = 2.159e+07
  steps = 80, shift = 13.8, angle = 3.88 degrees
Position of A.map (#1) relative to B.map (#0) coordinates:
  Matrix rotation and translation
    -0.31907565  -0.94727261   0.02941662 968.10738925
     0.94766668  -0.31925750  -0.00158170 561.43029040
     0.01088978   0.02737247   0.99956599  -7.05144295
  Axis   0.01527722   0.00977540   0.99983551
  Axis point 282.50181304 628.39781990   0.00000000
  Rotation angle (degrees) 108.62565060
  Shift along axis  13.22791470

The other way is to open IDLE in Chimera (Tools/General Control).

Type:
om = chimera.openModels
mlist = om.list()
m = mlist[0] # First map. m = mlist[1] will get you the 2nd map
print m.openState.xform # 3x3 rotation matrix, ast column is translation

-0.841777 -0.53957 -0.0165966 1273.53
-0.538462 0.841438 -0.0451738 427.043
0.0383394 -0.0290897 -0.998841 1228.6

For un-translated & rotated map, your output will be like:
1 0 0 0
0 1 0 0
0 0 1 0

Look at more detail in here
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html to
understand Chimera's xform matrix.

Best,
Huy


On Wed, Jul 29, 2015 at 9:10 AM, Penczek, Pawel A <
Pawel.A.Penczek at uth.tmc.edu> wrote:

> Dear Sergej,
>
> Chimera offers reach environment for manipulation and alignment of EM
> maps.  To transfer the results
> to human-friendly format and to manipulate them further in SPARX you can
> use simple python
> scripts described here:
> http://sparx-em.org/sparxwiki/align_chimera
>
> They read Chimera orientation matrices and, if needed, apply
> transformations directly to EM maps.
>
> Regards,
> -
> Pawel Penczek
> pawel.a.penczek at uth.tmc.edu
>
>
>
>
> > On Jul 29, 2015, at 8:05 AM, Sergej Masich <Sergej.Masich at ki.se> wrote:
> >
> > Dear colleagues,
> >
> > 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.
> >
> > 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.
> >
> > 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?
> >
> > Any advice is appreciated. Thank you in advance.
> >
> > Sergej Masich
> > =============================
> > Dr. Sergej Masich
> > Dept. of Cell and Molecular Biology
> > Karolinska Institutet
> > Box 285
> > 171 77 Stockholm, Sweden
> > tel: (+)46 - 8 - 524 873 61
> > mobile: (+)46 - 736 - 833 693
> > e-mail: Sergej.Masich at ki.se
> >
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