Difference between revisions of "Modes"
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! NMA | ! NMA | ||
− | | [[Keywords#DEBUG | DEBUG]] [[Keywords# | + | | [[Keywords#DEBUG | DEBUG]] [[Keywords#EIGEN | EIGEN]] [[Keywords#ENSEMBLE | ENSEMBLE]] [[Keywords#JOBS | JOBS]] [[Keywords#KEYWORDS | KEYWORDS]] [[Keywords#MUTE | MUTE]] [[Keywords#NMAMODES | NMAMODES]] [[Keywords#NMAPDB | NMAPDB]] [[Keywords#ROOT | ROOT]] [[Keywords#TITLE | TITLE]] [[Keywords#VERBOSE | VERBOSE]] [[Keywords#XYZOUT | XYZOUT]] |
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! NCS | ! NCS | ||
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! MR_ATOM | ! MR_ATOM | ||
− | | [[Keywords#ATOM | ATOM]] [[Keywords#CELL | CELL]] [[Keywords# | + | | [[Keywords#ATOM | ATOM]] [[Keywords#CELL | CELL]] [[Keywords#COMPOSITION | COMPOSITION]] [[Keywords#CRYSTAL | CRYSTAL]] [[Keywords#DEBUG | DEBUG]] [[Keywords#ELLG | ELLG]] [[Keywords#ENSEMBLE | ENSEMBLE]] [[Keywords#HKLIN | HKLIN]] [[Keywords#HKLOUT | HKLOUT]] [[Keywords#JOBS | JOBS]] [[Keywords#KEYWORDS | KEYWORDS]] [[Keywords#LLGCOMPLETE | LLGCOMPLETE]][[Keywords#MACANO | MACANO]] [[Keywords#MACMR | MACMR]] [[Keywords#MACSAD | MACSAV]] [[Keywords#MACTNCS | MACTNCS]] [[Keywords#MUTE | MUTE]] [[Keywords#NORMALIZATION | NORMALIZATION]] [[Keywords#PACK | PACK]] [[Keywords#PEAKS | PEAKS]] [[Keywords#PERMUTATIONS | PERMUTATIONS]] [[Keywords#PURGE | PURGE]] [[Keywords#REFLECTIONS | REFLECTIONS]] [[Keywords#RESCORE | RESCORE]] [[Keywords#RESOLUTION | RESOLUTION]] [[Keywords#ROOT | ROOT]] [[Keywords#SAMPLING | SAMPLING]] [[Keywords#SEARCH | SEARCH]] [[Keywords#SGALTERNATIVE | SGALTERNATIVE]] [[Keywords#SOLUTION | SOLUTION]] [[Keywords#SPACEGROUP | SPACEGROUP]] [[Keywords#TITLE | TITLE]] [[Keywords#TNCS | TNCS]] [[Keywords#TOPFILES | TOPFILES]] [[Keywords#VERBOSE | VERBOSE]] [[Keywords#XYZOUT | XYZOUT]] [[Keywords#ZSCORE | ZSCORE]] |
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Revision as of 11:16, 16 October 2012
Contents
- 1 Phaser Executable
- 2 Python Interface
- 3 Modes
- 3.1 Automated Molecular Replacement
- 3.2 Rotation Function
- 3.3 Translation Function
- 3.4 Packing
- 3.5 Refinement and Phasing
- 3.6 Anisotropy Correction
- 3.7 Translational NCS and Twin analysis
- 3.8 Cell Content Analysis
- 3.9 Normal Mode Analysis
- 3.10 Automated Experimental Phasing
- 3.11 Single Atom Molecular Replacement
- 4 Keywords Relevant to Each Mode
Phaser runs in different modes, which perform Phaser's different functionalities. Modes can either be basic modes or modes that combine the functionality of basic modes.
Phaser Executable
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the MODE keyword.
Python Interface
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. See Python Interface for details.
Modes
Automated Molecular Replacement
- MODE MR_AUTO
- Combines cell content analysis, anisotropy correction, translational NCS analysis, fast rotation and translation functions, and refinement and phasing to automatically solve a structure by molecular replacement
ResultMR r = runMR_AUTO(i=InputMR_AUTO)
Rotation Function
- MODE MR_ROT
- Combines the anisotropy correction, translational NCS analysis, and EITHER likelihood-enhanced fast rotation function, by default rescored with the full rotation likelihood function OR a brute-force search of angles using the full likelihood rotation function
ResultMR_RF r = runMR_FRF(i=InputMR_FRF)
Translation Function
- MODE MR_TRA
- Combines the anisotropy correction, translational NCS analysis, and EITHER likelihood-enhanced fast translation function, by default rescored by the full likelihood translation function OR a brute force search of positions using the full likelihood translation function to find the position of a previously oriented model
ResultMR_TF r = runMR_FTF(i=InputMR_FTF)
Packing
- MODE MR_PAK
- Determines whether molecular replacement solutions pack in the unit cell using a C-alpha clash test
ResultMR r = runMR_PAK(i=InputMR_PAK)
Refinement and Phasing
- MODE MR_RNP
- Combines the anisotropy correction, translational NCS analysis, and refinement against the likelihood function to optimize full or partial molecular replacement solutions and phase the data. At the end of refinement, the list of solutions is checked for duplicates, which are pruned
ResultMR r = runMR_RNP(i=InputMR_RNP)
Anisotropy Correction
- MODE ANO
- Corrects the experimental data (amplitude and associated sigma) for anisotropy. First, the anisotropy is removed by scaling up data from weak directions and scaling down data from strong directions, preserving the overall equivalent isotropic B-factor. Then (as suggested by Strong et al. (2006), PNAS 103:8060-8065), the data are resharpened to restore the original falloff in the strong direction. The amount of resharpening can be controlled with the RESHARP keyword.
ResultANO r = runANO(i=InputANO)
Translational NCS and Twin analysis
- MODE NCS
- Finds pseudo-translational NCS vectors and corrects the data for intensity variations due to the ptNCS using likelihood methods. The data are corrected for anisotropy first and analysed for twinning before and after data correction.
ResultNCS r = runNCS(i=InputNCS)
Cell Content Analysis
- MODE CCA
- Determines the composition of the crystals using the "new" Matthews coefficients of Kantardjieff & Rupp (2003) ("Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA and protein-nucleic acid complex crystals". Protein Science 12:1865-1871). The molecular weight of ONE complex or assembly to be packed into the asymmetric unit is given and the possible Z values (number of copies of the complex or assembly) that will fit in the asymmetric unit and the relative frequency of their corresponding VM values is reported.
ResultCCA r = runCCA(i=InputCCA)
Normal Mode Analysis
- MODE NMA
- Writes out pdb files that have been perturbed along normal modes, in a procedure similar to that described by Suhre & Sanejouand (Acta Cryst. D60, 796-799, 2004). Each run of the program writes out a matrix FILEROOT.mat that contains the eigenvectors and eigenvalues of the atomic Hessian, and can be read into subsequent runs of the same job, to speed up the analysis.
ResultNMA r = runNMA(i=InputNMA)
Automated Experimental Phasing
- MODE EP_AUTO
- Combines anisotropy correction, translational NCS analysis, cell content analysis, and SAD phasing to automatically solve a structure by experimental phasing
ResultEP r = runEP_AUTO(i=InputEP_AUTO)
Single Atom Molecular Replacement
- MODE MR_ATOM
- Combines automated molecular replacement with log-likelihood gradient completion to solve high resolution structures by single atom MR. The data are prepared with runMR_DAT and then the phasing is done withing the EP_AUTO mode.
ResultEP r = runMR_ATOM(i=InputMR_ATOM)