globsymm

• Manual
  • Introduction
  • Running GLOBSYMM
    • Command-Line Arguments and Options
    • 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

Usage:

$ globsymm [OPTIONS]

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

Command-Line Arguments and Options

ELLLIP 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

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

Screen Text	Default	Description
Output file	N/A	Project identifier, will be used as a prefix for all output file names
Enter file name, experimental data	N/A	The name of the data file containing the experimental SAXS profile of the oligomer.
Angular units in the input file : 4pisin(theta)/lambda [1/angstrom] (1) 4pisin(theta)/lambda [1/nm ] (2) 2* sin(theta)/lambda [1/angstrom] (3) 2* sin(theta)/lambda [1/nm ] (4)	1	Formula for the scattering vector in the data file and its units.
Fitting range in fractions of Smax	1.0	Percentage of the scattering curve to fit, starting at the first point. Default is the entire curve.
Amplitudes of a monomer	N/A	The name of the file with partial scattering amplitudes of the monomer computed byCRYSOL.
Symmetry: Pn(2)(n=2-6)	P222	Supported symmetries are:P2-P6, P222, P32-P62. The n-fold axis is Z, if there is in addition a two-fold axis it coincides with Y
Average distance from the origin	var	The search will be performed in the vicinity of specified value. The default is computed as a square root of the difference of the experimental radius of gyration squared and that from the monomer. This ensures proper R~g~value of the intact oligomer.
Spatial increment in angstroems	1.0	Step in the grid search of translations.
No of spatial steps in one direction	1	Number of steps along the radius towards the origin or in opposite direction.
Angular increment in degrees	5.0	Step in the grid search of rotations.
Number of angular steps	var	Number of clockwise (or counterclockwise) rotations. Default is 180/step.
Fibonacci grid order for positioning	12 for Pn2,1 for Pn	Translational search is done by moving the monomer along radial directions. The higher the order of the grid the more directions are considered. For Pn symmetries shifting along one axis (grid order=1) is enough to construct arbitrary multimer.
Fibonacci grid order for rotation axes	12	A separate grid of angular directions is generated as a set of rotational axes for the search of monomer’s orientation.
RMSD threshold for grouping solutions	var	During the run the program keeps a list of 20 best solutions, which are grouped after the minimization is finished. All solutions within the group must differ from the best model of this group by r.m.s.d. less than the specified threshold. The default value is 20% of the experimental R~g~.
String with the 1st atom in the pair	N/A	The string from the atomic coordinates file containing the Ca atom of the appropriate residue (for the residues making the contacts, if the oligomerization interface is known). This question may be asked several times. Empty string means termination of the input of the contacts information.
String with the 2nd atom in the pair	N/A	The string from the atomic coordinates file containing the Ca atom of the appropriate residue. This question may be asked several times. Empty string means termination of the input of the contacts information.
Contact distance	5.0	The desired maximal distance between the two residues. This question may be asked several times.
Contact weight	1.0	How much the Contacts Penalty shall influence the target function. A value of0.0disables the penalty. If unsure, use the default value. If the desired contacts are not observed, try increasing the weight.

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.

Extension	Description
.log	Contains the information about the modelling parameters and the resulting models. This file can be used to retrieve the kept solutions other than the best one (which is automatically saved).
-1.pdbor-1.cif	The current best model of oligomer in either PDB or mmCIF format. The header of the file contains information about the modelling parameters.
-1.fit	Fit of the current best model. Columns in the file are: ‘s’, ‘I~exp~’ and ‘I~oligomer~’.

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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