Difference between revisions of "Phaser-2.7 series changelog"
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(Created page with ";Phaser 2.7.0 * No functional changes from 2.6 series * Major changes to internal data structures :: Ensemble parameters either input or worked out on input ::: One point of c...") |
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− | ;Phaser 2.7.0 | + | ;Phaser-2.7.12 |
+ | *GIMBLE refinement, which splits ensembles by chain for rigid body refinement | ||
+ | *automatic tNCS NMOL determination in presence of commensurate modulation | ||
+ | *bugfixes | ||
+ | : input solution list checked for pass of intrinic TF packing test | ||
+ | : ensembles can refine to zero occupany in pruning | ||
+ | ;Phaser-2.7.11 | ||
+ | *additional peak clustering selection/annotation functionality PEAK ... LEVEL | ||
+ | *search deep only implemented for auto fast mode, not for FRF mode | ||
+ | *packing test during FTF run by default with 50% pairwise packing cutoff | ||
+ | *bugfixes | ||
+ | : stored solution list does not carry phasing arrays excessive memory | ||
+ | : occupancy refinement takes account of VRMS | ||
+ | ;Phaser-2.7.10 | ||
+ | *option to run packing test during FTF so as to eliminate non-packing translations from top | ||
+ | *packing test during FTF run by default for helices | ||
+ | *(selected) obsoleted keywords don't throw error reported as warning in logfile | ||
+ | *bugfixes | ||
+ | : peak search percent for translation function | ||
+ | ;Phaser-2.7.9 | ||
+ | *replace unweighted 2nd moments by inverse variance-weighted 2nd moments for twinning tests | ||
+ | *pairwise packing by percent only, other packing modes obsoleted | ||
+ | *PAK reported in annotiation is maximum percent overlap amongst solution set | ||
+ | *bugfixes | ||
+ | : use of input trace molecule | ||
+ | ;Phaser-2.7.8 | ||
+ | *Speed up packing test to O(N) | ||
+ | *bugfixes | ||
+ | : correctly increase scattering with implausible composition | ||
+ | ;Phaser-2.7.7 | ||
+ | *write tNCS and anisotropy parameters to binary files (on user request) | ||
+ | *read TNCS/anisotropy binary files to avoid refinement, when running through scripts | ||
+ | ;Phaser-2.7.6 | ||
+ | *account for measurement error in eLLG calculation | ||
+ | *rigid body refinement can separate chains in ensembles with MACMR CHAINS ON | ||
+ | ;Phaser-2.7.5 | ||
+ | *change Vm probabilities to Weichenberger & Rupp 2013 from Kantardjieff & Rupp 2003 | ||
+ | *CCA accounts for PROTEIN/NUCLEIC/MIXED compositions different Vm probabilities | ||
+ | ;Phaser-2.7.4 | ||
+ | *packing trace molecule can be entered independently of coordinates and map | ||
+ | *packing volume for maps calculated using Wang mask algorithm | ||
+ | *packing test by PAIRWISE only considers pairwise overlaps, not global overlap | ||
+ | *packing sampling can be forced to ALL, CALPHA, HEXGRID or AUTO (default AUTO) | ||
+ | *obsoleted packing test by BEST | ||
+ | *automatic search number for single search ensemble | ||
+ | *bugfixes | ||
+ | : RMS from ID estimator function parameters (A,B,C) did not match published parameters | ||
+ | : negative variance when trying to amalgamate many solutions with negative B-factors | ||
+ | : chain overlap incorrectly detected for nucleic acid | ||
+ | ;Phaser-2.7.3 | ||
+ | *improve tests for RMS correlations between members of an ensemble | ||
+ | ;Phaser-2.7.2 | ||
+ | *determine number of (average scattering) residues required to achieve target eLLG | ||
+ | *bugfixes | ||
+ | : header for Rotation Gyration Refinement mode corrected | ||
+ | ;Phaser-2.7.1 | ||
+ | *selection by CHAIN and MODEL for PDB coordinate entry | ||
+ | *concatenation of PDB files on ENSEMBLE keyword input obsoleted | ||
+ | *occupancy refinement operates on single model, not ensembles | ||
+ | *change to format of SOLUTION HISTORY | ||
+ | *change to SOLUTION variance card, only parse/unparse DRMS | ||
+ | *bugfixes | ||
+ | : only use solutions that pack to determine top LLG for purge after refinement | ||
+ | : occupancy refinement using ensembles failing various asserts in some circumstances | ||
+ | : exclude solutions that fail to pack from duplicate test after refinement | ||
+ | : incorrect selection of best model when CARD ON input used sequence identity | ||
+ | : reporting negative contrast (Cntrst) for LLG near purge mean | ||
+ | : bugs in FAST mode solution reversion with pruning | ||
+ | ;Phaser-2.7.0 | ||
* No functional changes from 2.6 series | * No functional changes from 2.6 series | ||
− | * | + | *new internal data structures for ensembles |
− | : | + | : ensemble parameters either input or worked out on input |
− | + | : Indexing of values in ensemble/model arrays consistent | |
− | + | *introduce command line flag --changelog gives changelog and bugfixes from previous version | |
− | + | : formal tracking of changes | |
− | + | *bugfixes | |
− | + | : Wilson B-factor not being carried internally or used correctly for output pdb files | |
− | * | + | : ID being used as RMS is eLLG calculation in MODE MR_FRF |
− | : |
Revision as of 12:56, 4 August 2016
- Phaser-2.7.12
- GIMBLE refinement, which splits ensembles by chain for rigid body refinement
- automatic tNCS NMOL determination in presence of commensurate modulation
- bugfixes
- input solution list checked for pass of intrinic TF packing test
- ensembles can refine to zero occupany in pruning
- Phaser-2.7.11
- additional peak clustering selection/annotation functionality PEAK ... LEVEL
- search deep only implemented for auto fast mode, not for FRF mode
- packing test during FTF run by default with 50% pairwise packing cutoff
- bugfixes
- stored solution list does not carry phasing arrays excessive memory
- occupancy refinement takes account of VRMS
- Phaser-2.7.10
- option to run packing test during FTF so as to eliminate non-packing translations from top
- packing test during FTF run by default for helices
- (selected) obsoleted keywords don't throw error reported as warning in logfile
- bugfixes
- peak search percent for translation function
- Phaser-2.7.9
- replace unweighted 2nd moments by inverse variance-weighted 2nd moments for twinning tests
- pairwise packing by percent only, other packing modes obsoleted
- PAK reported in annotiation is maximum percent overlap amongst solution set
- bugfixes
- use of input trace molecule
- Phaser-2.7.8
- Speed up packing test to O(N)
- bugfixes
- correctly increase scattering with implausible composition
- Phaser-2.7.7
- write tNCS and anisotropy parameters to binary files (on user request)
- read TNCS/anisotropy binary files to avoid refinement, when running through scripts
- Phaser-2.7.6
- account for measurement error in eLLG calculation
- rigid body refinement can separate chains in ensembles with MACMR CHAINS ON
- Phaser-2.7.5
- change Vm probabilities to Weichenberger & Rupp 2013 from Kantardjieff & Rupp 2003
- CCA accounts for PROTEIN/NUCLEIC/MIXED compositions different Vm probabilities
- Phaser-2.7.4
- packing trace molecule can be entered independently of coordinates and map
- packing volume for maps calculated using Wang mask algorithm
- packing test by PAIRWISE only considers pairwise overlaps, not global overlap
- packing sampling can be forced to ALL, CALPHA, HEXGRID or AUTO (default AUTO)
- obsoleted packing test by BEST
- automatic search number for single search ensemble
- bugfixes
- RMS from ID estimator function parameters (A,B,C) did not match published parameters
- negative variance when trying to amalgamate many solutions with negative B-factors
- chain overlap incorrectly detected for nucleic acid
- Phaser-2.7.3
- improve tests for RMS correlations between members of an ensemble
- Phaser-2.7.2
- determine number of (average scattering) residues required to achieve target eLLG
- bugfixes
- header for Rotation Gyration Refinement mode corrected
- Phaser-2.7.1
- selection by CHAIN and MODEL for PDB coordinate entry
- concatenation of PDB files on ENSEMBLE keyword input obsoleted
- occupancy refinement operates on single model, not ensembles
- change to format of SOLUTION HISTORY
- change to SOLUTION variance card, only parse/unparse DRMS
- bugfixes
- only use solutions that pack to determine top LLG for purge after refinement
- occupancy refinement using ensembles failing various asserts in some circumstances
- exclude solutions that fail to pack from duplicate test after refinement
- incorrect selection of best model when CARD ON input used sequence identity
- reporting negative contrast (Cntrst) for LLG near purge mean
- bugs in FAST mode solution reversion with pruning
- Phaser-2.7.0
- No functional changes from 2.6 series
- new internal data structures for ensembles
- ensemble parameters either input or worked out on input
- Indexing of values in ensemble/model arrays consistent
- introduce command line flag --changelog gives changelog and bugfixes from previous version
- formal tracking of changes
- bugfixes
- Wilson B-factor not being carried internally or used correctly for output pdb files
- ID being used as RMS is eLLG calculation in MODE MR_FRF