Famos - Revision history

Rdo20: /* Usage from the command line */

2016-09-08T16:45:25Z

‎Usage from the command line

Rdo20: /* Algorithm */

2016-09-08T16:43:25Z

‎Algorithm

Rdo20: /* Output */

2016-09-08T16:42:51Z

‎Output

Rdo20: /* Examples of PHIL input */

2016-09-08T16:42:17Z

‎Examples of PHIL input

Rdo20: /* Algorithm */

2016-09-08T16:40:13Z

‎Algorithm

Rdo20: /* Examples of PHIL input */

2016-09-08T16:31:50Z

‎Examples of PHIL input

Rdo20: /* Examples of PHIL input */

2016-09-08T16:30:58Z

‎Examples of PHIL input

Rdo20: /* Usage from the command line */

2016-09-08T16:17:44Z

‎Usage from the command line

Rdo20: /* Usage from the command line */

2016-09-08T16:17:15Z

‎Usage from the command line

Rdo20: /* Command line */

2016-09-08T16:13:01Z

‎Command line

@@ Line 19: / Line 19: @@
 '''phaser.famos''' uses [https://www.phenix-online.org/documentation/file_formats.html#phil-files-eff-def-phil Phenix PHIL input] in either a text file or as keywords like:
-   phaser.famos moving.pdb=pdbfile1 fixe.pdb=pdbfile2
+   phaser.famos moving.pdb=pdbfile1 fixed.pdb=pdbfile2
 or:

@@ Line 130: / Line 130: @@
 ==Algorithm==
-phaser.famos 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:
+'''phaser.famos''' 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))) - log(0.9)),
@@ Line 138: / Line 138: @@
 MLAD can loosely be interpreted as a distance measure between structures. But it is not a metric in a strict mathematical sense since the triangle inequality is not fulfilled. Unlike a plain root mean square deviation the logarithm in the MLAD formula will downplay contributions of atom pairs where the atoms are spatially distant. If an RMSD were employed such atom pairs would contribute on an equal footing with those groups of atom pairs that can be superposed perfectly. This in turn may lead to non-optimal superpositions when the structures tested against one another consists of multiple domains where one domain has undergone a domain motion, i.e. where a subset of atoms in one chain are bound to be spatially distant from the atoms in the other chain they have been paired with.
-phaser.famos 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.
+'''phaser.famos''' 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.
 ===Caveats===

@@ Line 122: / Line 122: @@
 ==Output==
-The 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 phaser.famos will output mulitple log files corresponding to each MR solution.
+The 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 '''phaser.famos''' will output mulitple log files corresponding to each MR solution.
 ===Do the MR solutions match?===

@@ Line 36: / Line 36: @@
 ===Examples of PHIL input===
-Unless the input just constitutes of two PDB files a PHIL file is the easiest way to enter input. A few examples of PHIL for phaser.famos are given below.
+Unless the input just constitutes of two PDB files a PHIL file is the easiest way to enter input. A few examples of PHIL for '''phaser.famos''' are given below.
 Testing a command-line Phaser MR solution file against a solution specified as a PDB file:

@@ Line 130: / Line 130: @@
 ==Algorithm==
-phaser.famos 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:
+phaser.famos 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))) - log(0.9)),
@@ Line 136: / Line 136: @@
 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. The factor log(0.9) is subtracted to ensure that MLAD(0) = 0.0, i.e. that two identical structures produces the value zero.
-MLAD can loosely be interpreted as a distance measure between structures. But it is not a metric in a strict mathematical sense since the triangle inequality is not fulfilled. Unlike a plain root mean square deviation the logarithm in the MLAD formula will downplay contributions of atom pairs where the atoms are spatially distant. If an RMSD were employed such contributions would contribute with the same amount as those atom pairs that can be superposed perfectly. This in turn may lead to incorrect super-positions when the chains tested against one another consists of multiple domains where one domain has undergone a domain motion, i.e. where a subset of atoms in one chain are bound to be spatially distant from the atoms in the other chain they have been paired with.
+MLAD can loosely be interpreted as a distance measure between structures. But it is not a metric in a strict mathematical sense since the triangle inequality is not fulfilled. Unlike a plain root mean square deviation the logarithm in the MLAD formula will downplay contributions of atom pairs where the atoms are spatially distant. If an RMSD were employed such atom pairs would contribute on an equal footing with those groups of atom pairs that can be superposed perfectly. This in turn may lead to non-optimal superpositions when the structures tested against one another consists of multiple domains where one domain has undergone a domain motion, i.e. where a subset of atoms in one chain are bound to be spatially distant from the atoms in the other chain they have been paired with.
 ===Caveats===

@@ Line 86: / Line 86: @@
+     }
+   }
    AltOrigSymMates.moving.mrsolution
+   {

@@ Line 64: / Line 64: @@
      pklfname = "testdata/phaser_mr_13.pkl"
+   }
    AltOrigSymMates.moving.pickle_solution
+   {

@@ Line 28: / Line 28: @@
 Examples:
-•Use the pdb file from one of the MR solutions in a scope. This is useful for simple cases such as when the solution comes from the PHENIX MRage GUI or when it is obtained from another MR program than Phaser.
+*Use the pdb file from one of the MR solutions in a scope. This is useful for simple cases such as when the solution comes from the PHENIX MRage GUI or when it is obtained from another MR program than Phaser.
-•Specify a Phaser MR solution by assigning the .sol file name of the solution to the mrsolution.solfname parameter of the sub-scope as well as assigning the IDs of the ensembles and the corresponding MR models to the parameters mrsolution.ensembles.name and mrsolution.ensembles.xyzfname. Multiple search components are specified as multiple ensembles. This way of specifying solutions is useful for solution files produced when Phaser is run from the command line and it produces several solutions of which one is the correct solution.
+*Specify a Phaser MR solution by assigning the .sol file name of the solution to the mrsolution.solfname parameter of the sub-scope as well as assigning the IDs of the ensembles and the corresponding MR models to the parameters mrsolution.ensembles.name and mrsolution.ensembles.xyzfname. Multiple search components are specified as multiple ensembles. This way of specifying solutions is useful for solution files produced when Phaser is run from the command line and it produces several solutions of which one is the correct solution.
-•Use a solution from the Phaser-MR GUI in PHENIX. In that case the parameter pickle.solution.pklfname in the sub-scope should be assigned to the solution file that is produced by PHENIX after an MR calculation. The pickle.solution.philfname should then be assigned to the input file for the MR calculation. This way of specifying solutions is useful when MR solutions are available from having run Phaser through the PHENIX interface.
+*Use a solution from the Phaser-MR GUI in PHENIX. In that case the parameter pickle.solution.pklfname in the sub-scope should be assigned to the solution file that is produced by PHENIX after an MR calculation. The pickle.solution.philfname should then be assigned to the input file for the MR calculation. This way of specifying solutions is useful when MR solutions are available from having run Phaser through the PHENIX interface.
-•If space group and the unit cell dimensions is not available from any of the input files then these need to be specified by assigning the parameter, spacegroupfname, either to a PDB file with a CRYST1 record or to an MTZ file with that information. This should be the data file used for the molecular replacement calculation.
+*If space group and the unit cell dimensions is not available from any of the input files then these need to be specified by assigning the parameter, spacegroupfname, either to a PDB file with a CRYST1 record or to an MTZ file with that information. This should be the data file used for the molecular replacement calculation.

@@ Line 25: / Line 25: @@
    phaser.famos 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:
+The PHIL input scopes, moving and fixed, specifies the MR solutions. Both scopes are programmatically equivalent and must be non-empty. This means that a scope should either specify the parameter xyzfname or the sub-scope mrsolution or the sub-scope pickle.solution.
-−
-*Assign the "moving.pdb" or "fixed.pdb" parameter to the pdb file from one of the MR solutions in question. This is useful for simple cases such as when the solution comes from the PHENIX MRage GUI is or when it is from a different MR program other than Phaser.
+Examples:
 ===Examples of PHIL input===

@@ Line 15: / Line 15: @@
 The superposed structure and the fixed structure can be visually inspected in a molecular viewer such as Coot or Pymol. Matches with low MLAD scores will have correspondingly good superpositions.
-==Command line==
+==Usage from the command line==
 '''phaser.famos''' uses [https://www.phenix-online.org/documentation/file_formats.html#phil-files-eff-def-phil Phenix PHIL input] in either a text file or as keywords like: