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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS

FLEXBIN manual

FLEXBIN

Written by M.V. Petoukhov
Post all your questions about FLEXBIN to the ATSAS Forum.

© ATSAS Team, 2018-2019

Table of Contents

Manual

The following describes the method implemented in FLEXBIN, details of the dialog prompt as well as the required input and the produced output files.

Introduction

FLEXBIN 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 FLEXBIN

Interactive Configuration

FLEXBIN can only be run in the dialog mode, no command line arguments are accepted.

FLEXBIN interactive prompt:

Screen TextDefaultDescription
Log file name N/A Project identifier, will be used as a prefix for all output file names.
Experimental data file name:  <dat> N/A The name of the data file containing the experimental SAXS profile.
First subunit PDB list:  <txt> N/A List file name with the conformers PDBs for the 1st subunit.
Second subunit PDB list:  <txt> N/A List file name with the conformers PDBs for the 2nd subunit.
1st subunit contacting residue 0 Residue of the first subunit (Cα atom ordial number) at the interface with the second subunit. If zero, no further input is required.
2nd subunit contacting residue 0 Residue of the second subunit (Cα atom ordial number) at the interface with the first subunit. This question is only asked if the first subunit residue is not 0
Contacting distance 0.0 Maximal distance between the residues of the first and the second subunits This question is only asked if the first subunit residue is not 0

Runtime Output

On 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:

FieldDescription
j Step number. Starts at 1, increases monotonically.
T Temperature measure, starts at an arbitrary high value, decreases each step by the annealing schedule factor.
Suc Number of successful mutations in this temperature step. Limited by the minimum and maximum number of successes. The number of successes should slowly decrease, the first couple of steps should be terminated by the maximum number of successes criterion. If instead the maximum number of iterations are done, or the number of successes drops suddenly by a large amount, the system should probably be cooled more slowly.
Eva Accumulated number of function evaluations.
CPU Elapsed wall-clock time since the annealing procedure was started.
F The best target function value obtained so far.
Pen Accumulated penalty value of the best target function.
The best chi^2 values The χ2 value of the best target function is given.

FLEXBIN Input Files

FLEXBIN 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 Files

After 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.

ExtensionDescription
.log Contains the same information as the screen output and is updated during execution of the program.
.pdb The current model of the binary complex. The REMARK section of the file contains information about the application used and about the parameters of the model, e.g. penalties and χ.
.fit Fit of the scattering curve computed from the complex (subcomplex) versus the corresponding experimental data. Columns in the output file are: 's', 'Iexp' 'Errexp' and 'Icomp'.

Examples

Constructing a Binary Complex

A 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
 ...


  Last modified: October 29, 2019

© BioSAXS group 2019