• Manual
  • Introduction
  • Running GLOBSYMM
    • Command-Line Arguments and Options
    • Interactive Configuration
    • Runtime Output
  • GLOBSYMM Input Files
  • GLOBSYMM Output Files
• Examples

Manual

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

Introduction

GLOBSYMM builds symmetric oligomers from a single subunit by fitting their calculated scattering to experimental SAXS data.

At a high level, the program places one monomer in 3D (rotation + translation), applies the chosen symmetry to generate all copies, computes the theoretical scattering of the resulting assembly, and calculates the fit to the data. This process is repeated over many candidate arrangements using an efficient grid search; models with clashes or disconnected subunits are penalized, and optional residue–residue contact information can be used to guide the search.

The result of GLOBSYMM is a ranked list of symmetric arrangements with the best-fitting model saved together with its calculated fit, and additional top solutions available for retrieval from the log.

Running GLOBSYMM

Usage:

$ globsymm [OPTIONS] [<LOGFILE> <SOLUTION_NUMBER>]

OPTIONS known by GLOBSYMM are described in next section. The configuration is done in full interactive mode.

Command-Line Arguments and Options

GLOBSYMM recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.

Modelling with GLOBSYMM is done in interactive dialog mode. Retrieval of non- best solutions is performed from the command line.

Interactive Configuration

Modelling with GLOBSYMM is done in interactive dialog mode.

An may be used to record and replay configurations, enabling repeatable runs without re-entering parameters.

Runtime Output

On runtime, the progress, the current value of the target function and the elapsed time are displayed:

  22% done, fVal =   3.87015, CPU =    7 sec

When the minimization procedure is finished the number of grid steps done and the number of skipped (overlapping or not interconnected) configurations are shown:

Total number of steps done ............................. : 1716
Number of structures skipped ........................... : 1695

GLOBSYMM Input Files

GLOBSYMM requires experimental SAS data (.dat) as well as binary amplitude data (.alm) of the monomer, as calculated by CRYSOL.

GLOBSYMM Output Files

GLOBSYMM 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.

To retrieve a model from the list of the kept models (in the log file), a command has to be executed:

$ globsymm LOGFILE SOLUTION

LOGFILE is the name of the generated log file and SOLUTION is the solution number. The SOLUTION.pdb and SOLUTION.fit files will be produced.

Examples

Tetrameric pyruvate decarboxilase from Z.mobilis with P222 symmetry

 Output file ............................ <         .log >: pdc01
 Enter file name, experimental data ..... <         .dat >: zymz
 Angular units in the input file :
 4*pi*sin(theta)/lambda [1/angstrom] (1)
 4*pi*sin(theta)/lambda [1/nm      ] (2)
 2*   sin(theta)/lambda [1/angstrom] (3)
 2*   sin(theta)/lambda [1/nm      ] (4)  <            1 >:
 Angular units multiplied by ............................ : 1.000
 Fitting range in fractions of Smax ..... <        1.000 >:
 Number of experimental points found .................... : 51
 Experimental radius of gyration ........................ : 37.82
 Number of points in the Guinier Plot ................... : 9
 Amplitudes, fixed particle ............. <         .alm >: z100
 Radius of gyration of the subunit ...................... : 26.17
 Maximum order of harmonics ............................. : 15
 Number of points in partial amplitudes ................. : 51
  Theoretical  points from            1     to           22    used
 Symmetry: Pn(2) (n=2-6) ................ <         P222 >:
 Average distance from the origin ....... <        27.30 >:
 Spatial increment in angstroems ........ <        1.000 >:
 No of spatial steps in one direction ... <            1 >:
 Angular increment in degrees ........... <        5.000 >:
 Number of angular steps ................ <           36 >:
 Fibonacci grid order for positioning ... <           12 >:
 Fibonacci grid order for rotation axes . <           12 >:
 RMSD threshold for grouping solutions .  <        7.563 >:
  Interatomic contacts information:
  Paste the strings of the monomer pdb file
  containing the atoms forming the pairs
  or press enter to skip further input
  Pair #            1
 String with the 1st atom in the pair ....................:

  Minimization started. Please wait...

 ALMGRZ --- :  110976 summation coefficients used

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