Phenix: Difference between revisions

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== Maps ==
== Maps ==
* phenix.maps - a command line tool to compute various maps. Seems to have no specific documentation. Can do B-factor sharpening for improving low-resolution maps.
 
* phenix.real_space_correlation - compute correlation between two maps; can work with ensembles of structures. Seems to have no specific documentation.
=== phenix.maps - a command line tool to compute various maps ===
* [http://www.phenix-online.org/documentation/get_cc_mtz_mtz.htm phenix.get_cc_mtz_mtz] -  
Seems to have no specific documentation. Can do B-factor sharpening for improving low-resolution maps.
* phenix.fobs_minus_fobs_map - calculate difference density. Seems to have no specific documentation.
 
* [http://www.phenix-online.org/documentation/multi_crystal_average.htm phenix.multi_crystal_average] -
=== phenix.real_space_correlation - compute correlation between two maps ===
* phenix.grow_density - local density improvement, as originally described in Acta Cryst. (1997). D53, 540-543 (in development). Seems to have no specific documentation.
Can work with ensembles of structures. Seems to have no specific documentation.
 
=== [http://www.phenix-online.org/documentation/get_cc_mtz_mtz.htm phenix.get_cc_mtz_mtz] ===
   
=== phenix.fobs_minus_fobs_map - calculate difference density ===
Seems to have no specific documentation.
 
=== [http://www.phenix-online.org/documentation/multi_crystal_average.htm phenix.multi_crystal_average] ===
=== phenix.grow_density - local density improvement ===
As originally described in Acta Cryst. (1997). D53, 540-543 (in development). Seems to have no specific documentation.


== NCS usage ==
== NCS usage ==
* [http://www.phenix-online.org/documentation/find_ncs.htm phenix.find_ncs] - identification of NCS operators from protein coordinates (chains), heavy atom coordinates, or a density map
=== [http://www.phenix-online.org/documentation/find_ncs.htm phenix.find_ncs] - identification of NCS operators ===
* phenix.superpose_maps - transforms maps following a molecular superposition. Seems to have no specific documentation.
from protein coordinates (chains), heavy atom coordinates, or a density map
* [http://www.phenix-online.org/documentation/apply_ncs.htm phenix.apply_ncs] - applying NCS to a molecule to generate all NCS copiea
 
=== phenix.superpose_maps - transforms maps following a molecular superposition ===
Seems to have no specific documentation.
 
=== [http://www.phenix-online.org/documentation/apply_ncs.htm phenix.apply_ncs] - applying NCS to a molecule to generate all NCS copies ===


== Model analysis and manipulation ==
== Model analysis and manipulation ==
* [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics; e.g. <font face="Courier">phenix.pbdtools your_model.pdb --show-adp-statistics</font> will show you complete statistics about B-factors; <font face="Courier">phenix.pbdtools your_model.pdb --show-geometry-statistics</font> will show you complete statistics about stereochemistry, <font face="Courier">phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" </font>- this will set all B=25 for all CA atoms in all ALA residues of chain A.
=== [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics ===
* [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model
e.g.  
* [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models
phenix.pbdtools your_model.pdb --show-adp-statistics
will show you complete statistics about B-factors;  
phenix.pbdtools your_model.pdb --show-geometry-statistics
will show you complete statistics about stereochemistry,
phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA"  
will set all B=25 for all CA atoms in all ALA residues of chain A.
 
=== [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model ===
=== [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models ===


== Validation ==
== Validation ==
* [http://www.phenix-online.org/documentation/validation.htm#anch14 phenix.polygon] - starts the GUI and runs calculations resulting in a [http://dx.doi.org/10.1107/S0907444908044296 POLYGON] drawing of important characteristics of your PDB file in relation to the data
 
* phenix.validate_model and phenix.validate are also GUI-only
=== [http://www.phenix-online.org/documentation/validation.htm#anch14 phenix.polygon] ===
* phenix.ramalyze, phenix.rotalyze, and phenix.cbetadev
starts the GUI and runs calculations resulting in a [http://dx.doi.org/10.1107/S0907444908044296 POLYGON] drawing of important characteristics of your PDB file in relation to the data
* phenix.clashscore
 
=== phenix.validate_model and phenix.validate ===
are also GUI-only
 
=== phenix.ramalyze, phenix.rotalyze, and phenix.cbetadev ===
 
=== phenix.clashscore ===


== See also ==
== See also ==
1,330

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