[Chimera-users] locating models in maps by unit cell transformations

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 5 10:10:20 PST 2008

Hi Trevor,
I don't know whether this will meet your needs or not, but you could  
try using Unit Cell (under Tools... Higher-Order Structure):

It will generate additional copies using MTRIX, SMTRY and/or CRYST1  
matrices. I am hoping the refmac map will go along with one of those  
copies, but a disadvantage of the approach is that you will have the  
other copies too (could tax the system depending on number/size).   
The extras could be removed after you get the copy you want, however.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 4, 2008, at 6:36 AM, Trevor Sewell wrote:

> Hi,
> It often turns out that the atomic model you create in O needs to  
> be transformed by a crystallographic symmetry operation in order to  
> fit into the map created by refmac. In O this is no problem because  
> the map automatically covers the bit of model you put in the center  
> of your screen. However this does not seem to happen in Chimera. Is  
> there an easy way to make the map cover the model (i.e. without  
> working out what the transformation is and then creating a  
> transformed pdb file)?
> Many thanks
> Trevor

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