[3dem] Manual alignment of density maps

[Penczek, Pawel A]

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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