[3dem] Manual alignment of density maps

[Michael Saur]

Hi Sergej,

for storing the new location and orientation of a map you could resample it in Chimera. I don’t know if it is the only option to do it (in Chimera), but if you move a first map and align it to a second map that has not been moved (as in moved separately from other models; if all models are active this doesn’t qualify as movement here) you can type

vop resample #[moved map] ongrid #[map that has not been moved] update true

into the Chimera command line

A new third map will open (copy of the first one) which will have a resampled coordinate system and will be at the same place as the second map when you re-open it. This way you don’t have to move the models every time you open them. 

Cheers,

Michael

------------------------------------------------------------
                                                                          
    Michael Saur, Dr. rer. nat.                           
    
    Max Planck Institute for Molecular Physiology                                                                    
    Otto-Hahn-Straße 11
    Room B2.25                                        
    44227 Dortmund

    Phone: +49 231 - 133 2312                   
    E-mail: michael.saur at mpi-dortmund.mpg <mailto:michael.saur at mpi-dortmund.mpg>.de                

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> On 29. 07. 2015, at 15:05, 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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