[Chimera-users] periodic shift of data in a Cryo EM map

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 22 09:18:53 PST 2013


Hi Ben,
Sounds like you want the command "vop cover"  -- it extends a map to cover specified atoms or to fill a specified box, using map periodicity and any symmetries.  For details, including how to assign map symmetries, please see:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 22, 2013, at 6:07 AM, Benjamin SCHWARZ wrote:

> Hi list,
>    Sorry for the inaccurate vocabulary, I am not really from the field. I'll try to be as descriptive as I can.
> 
> My problem is that I have a cryo EM map of a protein complex with the information somehow "shifted" in the "outline box". It looks like the center of my complex was placed on one corner of the outline box, and that the whole complex is thus spread over the 8 corners of the box… All the information is thus present in the map but should be periodically translated in order to place the center of my complex in the center of the box.
> 
> I can think of two ways to solve my problem, and for both I need your help :
> 	1. how to shift periodically the content of a map ?
> 	2. how to create a new (and bigger) map by repeating and translating one map in the 9 surrounding directions ?
> 
>    Thanks in avance
>          --Ben




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