[phenixbb] smaller the cell parameter of EM map

[dancingdream at 163.com]

Perfect! This problem bothering me for so long was finally solved! 
Thank you very much for your help!








--

Wei Ding
P.O.Box 603
The Institute of Physics,Chinese Academy of Sciences
Beijing,China
100190
Tel: +86-10-82649083
E-mail: dingwei at iphy.ac.cn


在 2018-12-30 00:43:01，"Pavel Afonine" <pafonine at lbl.gov> 写道：
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 at 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 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.

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 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!


Wei








 




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