[phenixbb] smaller the cell parameter of EM map
pafonine at lbl.gov
Sat Dec 29 08:43:01 PST 2018
have a look at the documentation:
Reading through it I find this
phenix.map_box map.mrc density_select=true
should do it. Let us know if it doesn't.
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
> 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
> 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!
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> Unsubscribe:phenixbb-leave at phenix-online.org
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