[phenixbb] smaller the cell parameter of EM map

[Pavel Afonine]

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 <mailto:wangli at moon.ibp.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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>
>

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