GLOBSYMM manual

Written by M.V. Petoukhov and D.I. Svergun.
Post all your questions about GLOBSYMM to the ATSAS Forum.

© ATSAS Team, 2003-2009

Table of Contents

• Manual
  • Introduction
  • Running GLOBSYMM
    • Interactive Configuration
    • Runtime Output
  • GLOBSYMM Input Files
  • GLOBSYMM Ouput Files
• Example

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.

GLOBSYMM implements the algorithm described by Petoukhov, M.V. & Svergun, D.I. (2005) "Global rigid body modeling of macromolecular complexes against small-angle scattering data." Biophys J. 89, 1237-1250.

Introduction

GLOBSYMM performs a global search of the quaternary structure of a symmetric oligomer built from identical monomers (point symmetries Pnk, where n = 2...6, and k = 1, 2 are supported). Rotation of a monomer by the Euler angles Alpha, Beta, Gamma followed by its displacement by the vector r and generation of all symmetry mates permits one to construct an arbitrary symmetric oligomer.

The theoretical scattering pattern I(s) of oligomer is expressed using spherical harmonics from the partial scattering amplitudes of a single subunit A_lm(s) in the current position/orientation and taking into account the symmetry rules. The subunit's amplitudes in arbitrary arrangement depend on its scattering amplitudes in the reference positions and on three rotational and three translational parameters. The reference partial scattering amplitudes of the subunits have to be precomputed by the program CRYSOL.

An exhaustive grid search of the quaternary structury of the oligomer is performed in GLOBSYMM exploiting the fact that an arbitrary model can be described by up to max six rotatranslational parameters (only four for Pn). These parameters are optimized to minimize discrepancy between the calculated curve and the experimental data while avoiding disconnected configurations and those with steric clashes. Eventual information on the multimerization interfaces (in terms of contacting residues) can also be taken into account.

Please refer to the paper cited above for further details about the implemented algorithm.

Running GLOBSYMM

Interactive Configuration

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

GLOBSYMM interactive prompt:

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 uses the SAXS experimental data files (*.dat) in ascii format containing 3 columns: (1) experimental scattering vector, (2) experimental intensity and (3) experimental errors and binary files with partial scattering amplitudes of monomer computed 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.

Example

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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