[phenixbb] map calculation

Pavel Afonine PAfonine at lbl.gov
Wed Aug 27 10:43:59 PDT 2008

To compute the map:

phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1

For more details, look "Electron density maps" section of phenix.refine 



On 8/27/2008 9:53 AM, Chen Chen wrote:
> Dear all,
> I am having a question about map calcultation.
> I want to calculate a 2mFo-DFc map and a mFo-DFc map to 2.0 angstrom 
> from xxx.pdb and yyy.mtz, and zzz.cif should be supplied.
> Unit cell dimension and symmetry information is in the mtz file.
> It seems that phenix.maps can do the job, but I did not find a good 
> document on how to run it. In its help information, a parameter file is 
> needed.
> I tried do use parameter file for refinement, which has been 
> successfully used for phenix.refine, and I ran the command
> phenix.maps --unused_ok yyy.mtz xxx.pdb refine.param
> but phenix.maps report the error
> Traceback (most recent call last):
>   File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/command_line/maps.py", 
> line 7, in <module>
>     maps.run(args=sys.argv[1:])
>   File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 173, in run
>     log           = log)
>   File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 214, in 
> __init__
>     self.data = utils.determine_data(
> AttributeError: 'module' object has no attribute 'determine_data'
> Does anyonw know what I should do to get the maps?
> Thanks
> Chen

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