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Biological Small Angle Scattering |
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FLEXBIN manualWritten by M.V. Petoukhov © ATSAS Team, 2018-2019 Table of ContentsManualThe following describes the method implemented in FLEXBIN, details of the dialog prompt as well as the required input and the produced output files. IntroductionFLEXBIN performs quaternary structure modeling of a dimeric complex formed by flexible subunits with known atomic structures of multiple conformations against the SAXS data set. A simulated annealing protocol is employed to construct an interconnected ensemble of subunits without steric clashes, while minimizing the discrepancy between the experimental scattering data and the curves calculated from the appropriate subunits assemblies. At each step one of the conformers for both subunits is picked. The theoretical scattering patterns I(s) are expressed in terms of spherical harmonics from the partial scattering amplitudes of the subunits Alm(s) in their given positions and orientations. The subunit's amplitudes in arbitrary arrangement depend on its scattering amplitudes of the given conformer in the reference position and on three rotational and three translational parameters. Running FLEXBINInteractive ConfigurationFLEXBIN can only be run in the dialog mode, no command line arguments are accepted. FLEXBIN interactive prompt:
Runtime OutputOn runtime, two lines of output will be generated for each SA temperature step: j: 1 T: 10.0 Suc: 1000 Eva: 2164 CPU: 125. F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 The fields can be interpreted as follows, top-left to bottom-right:
FLEXBIN Input FilesFLEXBIN uses the SAXS experimental data files (*.dat) in ascii format containing 3 columns: (1) experimental scattering vector, (2) experimental intensity and (3) experimental errors; The list of the pdb files has the following format: 1F6M_r_u_pool_nr/st10-n1-n3-n1_trim.pdb 1F6M_r_u_pool_nr/st10-n1-n3-n2_trim.pdb 1F6M_r_u_pool_nr/st10-n1-n3-n3_trim.pdb 1F6M_r_u_pool_nr/st10-n1-n3-p1_trim.pdb 1F6M_r_u_pool_nr/st10-n1-p1-n2_trim.pdb 1F6M_r_u_pool_nr/st10-n2-n3-p1_trim.pdb 1F6M_r_u_pool_nr/st10-n2-n3-p2_trim.pdb 1F6M_r_u_pool_nr/st10-n2_trim.pdb 1F6M_r_u_pool_nr/st10-n3-n2-p3_trim.pdb 1F6M_r_u_pool_nr/st10-n3-n3-p2_trim.pdb 1F6M_r_u_pool_nr/st30-p3-n3-n1_trim.pdb 1F6M_r_u_pool_nr/st3-n3-n2-p3_trim.pdb FLEXBIN Output FilesAfter each simulated annealing step, FLEXBIN creates a set of output files, each filename starts with a customizable prefix that gets an extension appended. If a prefix has been used before, existing files will be overwritten without further note.
ExamplesConstructing a Binary ComplexA listing of questions/answers for a sample run is as follows: Log file name .......................... < .log >: test4 Experimental data file name ............ < .dat >: 1f6m Number of experimental points .......................... : 1695 Maximum s vector ....................................... : 0.4491 First subunit PDB list ................. < .txt >: 1F6M_r_u.txt Number of conformations, 1st ........................... : 12 Second subunit PDB list ................ < .txt >: 1F6M_l_u.txt Number of conformations, 2nd ........................... : 1 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n1-n3-n1_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: -0.041 -0.123 0.194 Number of atoms read ................................... : 2394 Initial center: 10.242 41.829 77.496 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n1-n3-n2_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For 14 zero directions radius 2.34 assumed Center of the excess electron density: -0.074 -0.178 0.155 Number of atoms read ................................... : 2394 Initial center: 10.242 41.829 77.495 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n1-n3-n3_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For 1 zero directions radius 2.34 assumed Center of the excess electron density: -0.005 -0.079 0.232 Number of atoms read ................................... : 2394 Initial center: 10.243 41.832 77.496 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n1-n3-p1_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For 19 zero directions radius 2.26 assumed Center of the excess electron density: 0.030 -0.162 0.192 Number of atoms read ................................... : 2394 Initial center: 10.245 41.829 77.495 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n1-p1-n2_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: -0.045 -0.187 0.120 Number of atoms read ................................... : 2394 Initial center: 10.243 41.827 77.495 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n2-n3-p1_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For 2 zero directions radius 2.09 assumed Center of the excess electron density: 0.006 -0.199 0.120 Number of atoms read ................................... : 2394 Initial center: 10.246 41.827 77.495 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n2-n3-p2_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: 0.023 -0.200 0.138 Number of atoms read ................................... : 2394 Initial center: 10.246 41.827 77.494 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n2_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: -0.007 -0.200 0.184 Number of atoms read ................................... : 2394 Initial center: 10.245 41.828 77.495 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n3-n2-p3_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: -0.031 -0.199 0.079 Number of atoms read ................................... : 2394 Initial center: 10.244 41.826 77.494 Computing X-ray Alms for 1F6M_r_u_pool_nr/st10-n3-n3-p2_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: -0.056 -0.182 0.122 Number of atoms read ................................... : 2394 Initial center: 10.243 41.827 77.494 Computing X-ray Alms for 1F6M_r_u_pool_nr/st30-p3-n3-n1_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: 0.131 -0.110 0.193 Number of atoms read ................................... : 2394 Initial center: 10.247 41.830 77.495 Computing X-ray Alms for 1F6M_r_u_pool_nr/st3-n3-n2-p3_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 2394 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: 0.010 -0.207 0.155 Number of atoms read ................................... : 2394 Initial center: 10.245 41.827 77.493 Computing X-ray Alms for 1F6M_l_u/1F6M_l_u_trim.pdb Read atoms and evaluate geometrical center ... Number of atoms read .................................. : 819 Percent processed 10 20 30 40 50 60 70 80 90 100 Processing atoms :>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Center of the excess electron density: -0.147 0.114 -0.012 Number of atoms read ................................... : 819 Initial center: -9.560 50.466 91.925 Initialized random seed as ..................... : 66696239186785092 Cross value ............................................ : 6.920 Discontiguity value .................................... : 0.0 1st subunit contacting residue ......... < 0 >: Total penalty .......................................... : 69.20 Chi-square ............................................. : 1684. ==== Simulated annealing procedure started ==== j: 1 T: 10.0 Suc: 1000 Eva: 2164 CPU: 125. F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 2 T: 9.00 Suc: 1000 Eva: 4595 CPU: 267. F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 3 T: 8.10 Suc: 1000 Eva: 7235 CPU: 420. F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 4 T: 7.29 Suc: 1000 Eva: 9855 CPU: 574. F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 5 T: 6.56 Suc: 1000 Eva: 12548 CPU: 729. F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 6 T: 5.90 Suc: 1000 Eva: 15447 CPU: 897. F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 7 T: 5.31 Suc: 1000 Eva: 18324 CPU: 0.106E+04 F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 8 T: 4.78 Suc: 1000 Eva: 21252 CPU: 0.123E+04 F: 1.879 Pen: 0.1190 The best chi^2 values: 1.8 j: 9 T: 4.30 Suc: 1000 Eva: 24298 CPU: 0.141E+04 F: 1.750 Pen: 0.000 The best chi^2 values: 1.7 ... |
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Last modified: October 29, 2019
© BioSAXS group 2019