Hi,

have a look at the documentation:

https://www.phenix-online.org/documentation/reference/map_box.html

Reading through it I find this

phenix.map_box map.mrc density_select=true

should do it. Let us know if it doesn't.

Pavel

On 12/29/18 07:46, dancingdream@163.com wrote:

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

Beijing,China

100190

Tel: +86-10-82649083
E-mail: dingwei@iphy.ac.cn

At 2018-12-29 15:30:51, "Pavel Afonine" <pafonine@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.

Pavel

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@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!

Wei

 

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