[Chimera-users] Script for positioning particles according the coordinates.

Tom Goddard goddard at sonic.net
Tue Feb 8 11:20:01 PST 2011

Hi Alex,

   There are two scripts (placem.py and place.py) on the Chimera Python 
scripts web page


that will place models at specified positions.  With the placem.py 
script you specify the models/maps to open and the x,y,z translations 
and optionally the rotation as a quaternion, one model on each line.  
You can repeat the same model.  The place.py script places multiple 
copies of a single model specifying translation and rotation using a 3 
by 4 matrix.


> Hi Tom,
> When I told about particles I meant electron-density maps (mrc, 
> spider, imagic or ccp4 formats). I know all orientation of the 
> particles and even more all of them a turned already -- what I need is 
> only to place all of them in exact positions. Of cause I can do it 
> manually, but it is bit boring.
> Thank you for the help in advance,
> Alex

> Dear colleagues,
> I would like to fit about 300 particles inside of the map according to 
> it coordinates (X,Y,Z) what I have found before.  Is it possible to 
> make this procedure automatically, such that program would load one 
> particle, shift it according to its coordinates (change pixel size if 
> necessary) and so on?
> Thank you in advance,
> Alexander

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