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phenix.find_alt_orig_sym_mate: Identify equivalent MR solutions of the same dataset irrespective of origin and symmetry operation
Author(s)
PurposeFor different molecular replacement (MR) solutions from the same dataset phenix.find_alt_orig_sym_mate.py finds for each chain in the moving solution the copy closest to chains in the fixed solution with respect to all symmetry operations and alternative origin shifts permitted by the spacegroup of the crystal. Usagephenix.find_alt_orig_sym_mate can be run from the command-line with PHIL input in either a text file or as keywords like phenix.find_alt_orig_sym_mate moving_pdb=pdbfile1 fixed_pdb=pdbfile2or phenix.find_alt_orig_sym_mate my_phil_input.txt.The PHIL input specifies the MR solution files either as "moving_pdb" and "fixed_pdb" or as the scopes, "moving" and "fixed". Both these scopes must hold valid content. The two scopes hold the parameter "xyzfname" and the sub-scopes "mrsolution" and "pickle_solution". For a scope to be valid one and only of the methods (1), (2) and (3) must be followed:
Examples of PHIL inputUnless the input just constitutes of two PDB files a PHIL file is the easiest way to enter input. A few examples of PHIL for phenix.find_alt_orig_sym_mate are given below. Testing a command-line Phaser MR solution file against a solution specified as a PDB file:
AltOrigSymMates.fixed.mrsolution
{
solfname = "testdata/MR_3ECI_A0_2P82_A0.sol"
ensembles
{
name = "MR_2P82_A0"
xyzfname = "testdata/sculpt_2P82_A0.pdb"
}
ensembles
{
name = "MR_3ECI_A0"
xyzfname = "testdata/sculpt_3ECI_A0.pdb"
}
}
AltOrigSymMates.moving_pdb="testdata/2z0d.pdb"
Testing two set of solution files from the PHENIX Phaser-MR GUI against one another:
AltOrigSymMates.fixed.pickle_solution
{
philfname = "testdata/phaser_mr_13.eff"
pklfname = "testdata/phaser_mr_13.pkl"
}
AltOrigSymMates.moving.pickle_solution
{
philfname = "testdata/phaser_mr_11.eff"
pklfname = "testdata/phaser_mr_11.pkl"
}
Testing two solution files from the command-line version of Phaser against one another:
AltOrigSymMates.fixed.mrsolution
{
solfname = "testdata/MR_3ECI_A0_2P82_A0.sol"
ensembles
{
name = "MR_2P82_A0"
xyzfname = "testdata/sculpt_2P82_A0.pdb"
}
ensembles
{
name = "MR_3ECI_A0"
xyzfname = "testdata/sculpt_3ECI_A0.pdb"
}
}
AltOrigSymMates.moving.mrsolution
{
solfname = "testdata/MR_2ZPN_A0_2P82_A0.sol"
ensembles
{
name = "MR_2P82_A0"
xyzfname = "testdata/sculpt_2P82_A0.pdb"
}
ensembles
{
name = "MR_2ZPN_A0"
xyzfname = "testdata/sculpt_2ZPN_A0.pdb"
}
}
AltOrigSymMates.spacegroupfname = "testdata/2Z0D.mtz"
For more information on the PHIL input see the bottom of this page. OutputThe closest match between chains in the moving section to chains in the fixed section is saved with the name of the pdb file in the fixed scope, concatenated with the name of the pdb file in the moving scope but prepended with "MinMLAD_". A log file with the name of the pdb file in the fixed scope, concatenated with the name of the pdb file in the moving scope but prepended with "AltOrigSymMLAD_" is written containing standard output. All files are saved in the current working directory. If MR solutions specified in the PHIL contains multiple solutions then phenix.find_alt_orig_sym_mate will output mulitple log files corresponding to each MR solution. Do the MR solutions match?A good match between two chains usually have a MLAD value below 1.5 whereas a bad match usually have a value above 2.0. This is a rule of thumb and exceptions do occur. It is advisable to visually inspect that the structures superpose one another in a molecular graphics viewing program. If the structures contain more chains and phenix.find_alt_orig_sym_mate did not place them all on the same origin a warning will be printed. Algorithmphenix.find_alt_orig_sym_mate computes configurations by looping over all symmetry operations and alternative origin shifts. An alignment between C-alpha atoms from moving_pdb and fixed_pdb is computed using secondary structure matching (SSM). If that fails or if the MLAD score achieved with SSM is larger than 2.0 an alignment is computed using MMTBX alignment functions which is part of the CCTBX. To estimate the best match a distance measure between the aligned C-alpha atoms is computed for each configuration. The mean log absolute deviation (MLAD) is defined as: MLAD(dR) = Σ( log(dr·dr/(|dr| + 0.9) + max(0.9, min(dr·dr,1)))), where dr is the difference vector between a pair of aligned C-alpha atoms and the sum is taken over all atom pairs in the alignment. MLAD is used as the distance measure. MLAD will downplay the contributions of spatially distant C-alpha atom pairs which may otherwise lead to incorrect matches when the space group has a floating origin and the chains tested against one another consists of large unaligned domains. phenix.find_alt_orig_sym_mate.py will for each chain in the fixed scope find the smallest MLAD with a copy of each chain in the moving scope for a given symmetry operation and alternative origin. When all chains in the fixed scope have been tested these copies will be saved to a file. For spacegroups with floating origin the minimum MLAD is found by doing a Golden Sectioning minimization along the polar axis for each copy of chains in moving_pdb. Also move HETATM (hetero atoms)Invoking this flag will move hetero atoms (ligands, waters, metals, etc.) in conjunction with their associated peptide chain. The program first invokes phenix.sort_hetatms as to associate hetero atoms sensibly with adjacent peptide chains. After having identified the transformation for a chain yielding the smallest MLAD score it then subjects the associated hetero atoms to the same transformation. Debug modeInvoking the debug flag produces individual pdb files of the C-alpha atoms used for each SSM alignment of the moving scope for each permitted symmetry operation and alternative origin. A gold atom is placed at the centroid of the C-alpha atoms. Similar files are produced for the fixed scope. These files are stored in a subfolder named "AltOrigSymMatesFiles". If a floating origin is present in the space group a table of MLAD values is produced by sliding a copy of the chains in the moving scope along the polar axis in the fractional interval [-0.5, 0.5] for each permitted symmetry operation and alternative origin. CaveatsThe program tests all solutions present in solution files entered as fixed scope against all solutions present in solution files entered as moving scope. Consequently the execution time is proportional to the number of solutions in fixed scope times the number of solutions in moving scope. The execution time is proportional to the number of SSM alignments being tested; if SSM identifies 12 alignments the program will take 12 times as long. ChangesThe command-line syntax mentioned in the Computational Crystallography Newsletter 2012 January has been replaced by PHIL syntax. Literature
Additional informationList of all find_alt_orig_sym_mate keywords
-------------------------------------------------------------------------------
Legend: black bold - scope names
black - parameter names
red - parameter values
blue - parameter help
blue bold - scope help
Parameter values:
* means selected parameter (where multiple choices are available)
False is No
True is Yes
None means not provided, not predefined, or left up to the program
"%3d" is a Python style formatting descriptor
-------------------------------------------------------------------------------
AltOrigSymMates
moving_pdb= None path to a PDB file from an MR solution
fixed_pdb= None path to a PDB file from an MR solution
spacegroupfname= None A PDB file with a CRYST1 record or an MTZ file
providing the space group and cell dimension for this
computation.
chosenorigin= "Any" By default all allowed origin shifts are probed.
Specifying "2/3, 1/3, 1/2" tells the program to
only explore symmetry operations for the unit cells displaced
at fractional positions (2/3, 1/3, 1/2)
use_all_SSM= False By default only the best sequence alignment from SSM is
used. Setting this value to True will include other suboptimal
alignments for testing.
no_symmetry_operations= False When set to False all symmetry operations are
probed during the computation.
movehetatms= False Move hetatoms close to a chain in conjunction with that
chain. Hetatoms are first associated with individual chains
with phenix.sort_hetatms before undergoing the same spatial
transformation as the chains.
debug= False
verbose= False
gui_output_dir= None For PHENIX GUI only.
job_title= None Job title in PHENIX GUI, not used on command line
moving Specify either mrsolution or pickle_solution.
mrsolution MR solution produced by command-line version of Phaser
solfname= None path to the solution file, i.e. the .sol file
ensembles Ensembles constituent in this MR solution. Typically these
are chains in the PDB file.
name= None ID for ensemble in the MR solution, i.e. the name after
the "SOLU 6DIM ENSE" string in the .sol file.
xyzfname= None Path to the PDB file with atoms representing this
ensemble. This is the search model used by Phaser for
this ensemble prior to solving the structure. It is not
the solved structure.
pickle_solution Phaser MR solution from PHENIX GUI
pklfname= None PHENIX GUI solution file from Phaser-MR, i.e. the .pkl
file
philfname= None PHENIX GUI configuration file used as input prior to
Phaser-MR, i.e. the .eff file
fixed Specify either mrsolution or pickle_solution.
mrsolution MR solution produced by command-line version of Phaser
solfname= None path to the solution file, i.e. the .sol file
ensembles Ensembles constituent in this MR solution. Typically these
are chains in the PDB file.
name= None ID for ensemble in the MR solution, i.e. the name after
the "SOLU 6DIM ENSE" string in the .sol file.
xyzfname= None Path to the PDB file with atoms representing this
ensemble. This is the search model used by Phaser for
this ensemble prior to solving the structure. It is not
the solved structure.
pickle_solution Phaser MR solution from PHENIX GUI
pklfname= None PHENIX GUI solution file from Phaser-MR, i.e. the .pkl
file
philfname= None PHENIX GUI configuration file used as input prior to
Phaser-MR, i.e. the .eff file
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