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.

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.

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 PDB 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 PDB 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 of 0.0 disables the penalty. If unsure, use the default
value. If the desired contacts are not observed, try increasing the weight.

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 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 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.

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).

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
...