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: [email protected] At 2018-12-29 15:30:51, "Pavel Afonine" 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, [email protected] 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 _______________________________________________ phenixbb mailing list [email protected]http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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: [email protected] 在 2018-12-30 00:43:01，"Pavel Afonine" 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, [email protected] 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: [email protected] At 2018-12-29 15:30:51, "Pavel Afonine" 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, [email protected] 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 _______________________________________________ phenixbb mailing list [email protected]http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]