[phenixbb] smaller the cell parameter of EM map

dancingdream at 163.com dancingdream at 163.com
Sat Dec 29 07:46:35 PST 2018

Thanks for the quick replay! 
But my case is that no homology model for the target protein and it should be built directly from the em map. What should I do in this case ?


Wei Ding
P.O.Box 603
The Institute of Physics,Chinese Academy of Sciences
Tel: +86-10-82649083
E-mail: dingwei at iphy.ac.cn

At 2018-12-29 15:30:51, "Pavel Afonine" <pafonine at lbl.gov> wrote:
Hi Wei,

cutting out a box with model and map around it may be a solution for your case. A tool for this is phenix.map_box or its GUI equivalent.


P.S.: phenix.real_space_refine does this internally so 'irrelevant' box size never affects runtime of refinement.

On 12/28/18 23:14, dancingdream at 163.com wrote:

Dear all,
The cell parameter of the EM map is always too large, which will make the model building program running very slow.
But in factor, the structure is a smal part of cell. So can I smaller the cell parameter when I use phenix.map_to_structure_factors to convert the EM map to mtz file.
Thank a lot!



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