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 subunit assemblies. At each step, one conformer for each subunit is selected
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 subunits’ amplitudes in an arbitrary arrangement depend on their 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 |
|---|---|---|
| Â | --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.
An interactive answers file (.ans) may be used to record and replay configurations, enabling repeatable runs without re-entering parameters.
| 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 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 (C-\(\alpha\) atom ordinal 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 (C-\(\alpha\) atom ordinal 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:
| Field | Description |
|---|---|
| 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 \(\chi^2\) values of the best target function are given. |
FLEXBIN Input Files
FLEXBIN expects background subtracted experimental SAS data (.dat) files.
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. |
| .pdb or .cif | Current model of the entire complex in either .pdb or .cif format, depending on model-format option. The comments section of the file contains information about the application used and about the parameters of the model, e.g. penalties and goodness-of-fit to the data \((\chi^2)\). |
| .fit | Fit of the scattering curve computed from a construct versus the corresponding experimental data. |
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
[...]
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
[...]