[phenixbb] on "Tutorial: Solving a structure with cryo-EM data using docking"

Pavel Afonine pafonine at lbl.gov
Wed Mar 17 15:36:29 PDT 2021

Hi Smith,

all data files that are used in tutorials are shipped with Phenix. So 
you don't need to download anything additionally. If you want to use 
your own data, just do it and follow the tutorial script. In this case 
your files have the same property as in the tutorial (for example, have 
symmetry if it is used as part of the tutorial).

Hope this helps!


On 3/13/21 18:29, Smith Lee wrote:
> Dear All,
> For "Tutorial: Solving a structure with cryo-EM data using docking", 
> it is easy to download the emd_20026_half_map_1_box.ccp4 and 
> emd_20026_half_map_2_box.ccp4 from the emd-20026 depositation, but 
> will you please let me know step by step how to get the tutorial used 
> seq.dat, 20026_auto_sharpen_A.ccp4 (any other name for this file? 
> Cannot find the exact name file  in emd_20026 depositation), 
> apoferritin_chainA_rsr.pdb (it mentioned "model refined against 
> sharpened map", which sharpened map, and what was the refinement 
> method ued?), run_denmod_dock.csh?
> I am looking forward to getting your reply.
> Best wishes,
> Smith
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