Phenix: Difference between revisions

655 bytes added ,  1 September 2011
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=== [http://www.phenix-online.org/documentation/xmanip.htm phenix.xmanip] - structure factor file manipulations ===
=== [http://www.phenix-online.org/documentation/xmanip.htm phenix.xmanip] - structure factor file manipulations ===


=== phenix.model_vs_data - statistics ===
=== [http://www.phenix-online.org/documentation/model_vs_data.htm phenix.model_vs_data] - statistics ===


not yet documented. Just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats. phenix.model_vs_data can output the map defined as:
Just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats. phenix.model_vs_data can output the map defined as:


[p][m]Fo+[q][D]Fc[kick][filled].
[p][m]Fo+[q][D]Fc[kick][filled].
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will list (among other things) map CC for all atoms or per residue.
will list (among other things) map CC for all atoms or per residue.
PDB deposition: phenix.model_vs_data model.pdb data.mtz will give B-factor statistics. Look for lines like this in the output:
      ADP (min,max,mean):
        all          (136 atoms): 4.4    97.6  25.3 
        side chains  (48 atoms): 4.9    96.8  21.0 
        main chains  (64 atoms): 4.4    97.6  28.3 
        macromolecule (112 atoms): 4.4    97.6  25.2 
        ligands      (1 atoms): 6.6    6.6    6.6 
        solvent      (23 atoms): 8.8    44.1  26.8 
      mean bonded (Bi-Bj) : 27.91
      number_of_anisotropic            : 0     
      number_of_non_positive_definite  : 0


=== phenix.real_space_correlation - statistics ===
=== phenix.real_space_correlation - statistics ===
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