flexbin
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 A~lm~(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
Usage:
$ flexbin [OPTIONS]
OPTIONS known by FLEXBIN are described in next section. The configuration is done in full interactive mode.
Command-Line Arguments and Options
FLEXBIN recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.
| Short Option | Long Option | Description |
|---|---|---|
| --model-format=<FMT> | Format of 3D models, one of: cif, pdb (default: cif) | |
| -h | --help | Print a summary of arguments, options, and exit. |
| -v | --version | Print version information and exit. |
Interactive Configuration
FLEXBIN can only be run in the dialog mode, no command line arguments are accepted. FLEXBIN interactive prompt:
| Screen Text | Default | Description |
|---|---|---|
| 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 1^st^subunit. |
| Second subunit PDB list: <txt> | N/A | List file name with the conformers PDBs for the 2^nd^subunit. |
| 1^st^subunit contacting residue | 0 | Residue of the first subunit (C~lpha~atom ordial number) at the interface with the second subunit. If zero, no further input is required. |
| 2^nd^subunit contacting residue | 0 | Residue of the second subunit (C~lpha~atom ordial number) at the interface with the first subunit. This question is only asked if thefirst subunit residueis not0 |
| Contacting distance | 0.0 | Maximal distance between the residues of the first and the second subunits This question is only asked if thefirst subunit residueis not0 |
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:
| Field | Description |
|---|---|
| j | Step number. Starts at 1, increases monotonically. |
| T | Temperature measure, starts at an arbitrary high value, decreases each step by theannealing schedule factor. |
| Suc | Number of successful mutations in this temperature step. Limited by theminimumandmaximumnumber of successes. The number of successes should slowly decrease, the first couple of steps should be terminated by themaximumnumber of successes criterion. If instead themaximum number of iterationsare 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\chi^2^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.
| Extension | Description |
|---|---|
| .log | Contains the same information as the screen output and is updated during execution of the program. |
| .pdbor.cif | The current model of the binary complex in either PDB or mmCIF format. The header section of the file contains information about the application used and about the parameters of the model, e.g. penalties and\chi^2^. |
| .fit | Fit of the scattering curve computed from the complex (subcomplex) versus the corresponding experimental data. Columns in the output file are: ‘s’, ‘I~exp~’ ‘Err~exp~’ and ‘I~comp~’. |
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
...