gasbor

• Manual
  • Introduction
    • Algorithm description
  • Running gasbor
    • Command-Line Arguments and Options
    • Interactive Configuration
    • Runtime Output
  • gasbor Input Files
  • gasbor Ouput Files
  • Limitations
• Examples
  • Lysozyme example
  • Transketolase example
  • Lysozyme with sequence
  • Gasbormx on Tetanus toxin
• References

Manual

Introduction

GASBOR is program for ab initio reconstruction of protein structure by a chain-like ensemble of dummy residues.

Algorithm description

The use of GASBOR is similar to that of DAMMIN or DAMMIF. Most of parameters have the same meaning. The most important difference is that the protein structure is represented not by dummy spheres on lattice (called dummy atoms in DAMMIN / DAMMIF, but not corresponding to real atoms), but rather by an ensemble of dummy residues (corresponding to average residue densities) placed anywhere in continuous space with a preferred number of close distance neighbours for each atom. The centers of these residues aim to approximate positions of the C-lpha atoms in the protein structure. The number of residues should be equal to that in the protein. Note, however, that these residues are anonymous, in the sense that their ordinal numbers in the model has nothing to do with the numbering primary sequence of the protein! Accordingly, the program does not subtract any Porod constant from the experimental data. In DAMMIN, it was recommended to discard high angle portions of the scattering patterns; in GASBOR, on the contrary, one should use them. The program is able to fit the data up to the resolution of 5 angstroms, i.e. momentum transfer s = 4 \pi *sin( heta )/ \lambda = 1.2 Å ^-1^.

Running gasbor

Command-Line Arguments and Options

Usage:

$ gasbor [GNOMFILE] [Num_DRs] [OPTIONS]

where gasbor should be replaced by the full program name (e.g. gasborp ). GASBOR accepts the following command line arguments:

Argument	Description
GNOMFILE	A relative or absolute path to aGNOM outputfile.
Num_DRs	Number of dummy residues in asymmetric part.

GASBOR recognizes the following command-line options.

Option	Description
–seed=<INT>	Set the seed for the random number generator
–mo<U	E>	Configuration mode, either User or Expert.
–lo<LOG_FILE>	Prefix to prepend to output filenames. Default is the name of theGASBOR input filewithout extension.
–model-format=<FMT>	Format of 3D models, one of: cif, pdb (default: cif)
–id<DESCRIPTION>	Project description. By default, the command line content is used.
–un<UNIT>	Angular unit of the input file, either 1 [1/Angstrom] or 2 [1/nm]; undefined by default.
–sy<SYMMETRY>	Specify the point symmetry of the particle. Point groups P1, …, P19, P_n_2 (n = 2, …, 12), P23, P432 orPICO(icosahedral) are supported. By default, no symmetry is enforced (P1).
–an<ANISOMETRY>	Particle anisometry:oblate(O),prolate(P) or_unknown_(default).
–dr<DIRECTION>	Direction of anisometry, applicable with P2 symmetry only:along(L),across(C) or_unknown_(default).
–help	Print usage information and exit.
–version	Print version information and exit.

Interactive Configuration

GASBOR reads in output files of GNOM. There are two versions of GASBOR, one performing the fit of the intensity in reciprocal space (GASBORI), and the other fitting the real space P(r) function (GASBORP). The algorithms of the two versions are similar. The reciprocal space version is slower but usually yields better fits to the experimental data. The real space version is much faster, and should be used when number of dummy residues makes runtime excessive (as runtime is proportional to square of number of dummy residues.) In addition, reciprocal space version is also available in implementation accounting for oligomeric equilibrium (GASBORMX). In this case, ab initio model of symmetric oligomer is built while assuming some fraction of monomers in solution (i.e. polydisperse sample). After starting GASBOR one may specify:

Prompt	Possible value(s)	Default value	Description
Computation mode	UserorExpert	User	After choosingExpertGASBOR will let you configure additionalexpert modeparameters.
InUserandExpertmode
Project identificator	lyz_or any other legal filename prefix_		Filename for log (here:lyz.log) and other output files.
Enter project description	_any text:_lysozyme at 3 mg/ml		Description that will be put into log file.
Totalnumberof curves to fit	1<integer<10	1	The question is only asked by GASBORMX which may fit a concentration series of oligomeric equilibrium.
Input data, GNOM output file name	_filename, like:_lyz.out		Input file with validGNOMoutput. If GASBOR doesn’t accept the file, then check thatGNOMrun has been finished and_P(r)_function written to the file. This question is asked for each curve, i.e. the number of times equals to thetotal number of curves to fitby GASBORMX.
Angular units in the input file	1	1	means that data unit isÅ^-1^
2	means that data unit is nm^-1^.
		This question is asked for each curve, i.e. the number of times equals to thetotal number of curves to fitby GASBORMX.
Portion of the curve to be fitted	0.001-1.0	1.0for entire curve	Whether curve should be fitted in entirety, or just a part of it. This question is asked for each curve, i.e. the number of times equals to thetotal number of curves to fitby GASBORMX.
Volume fraction of monomer (if known)	-1.0; (0.0, 1.0)	-1.0if unknown	If a positive number (below1.0) is given, such volume fraction of the monomer is kept fixed in the course of modelling. This question is only asked by GASBORMX.
Initial DRM	_filename, like:_gasbor.pdb	none	Enter, if you want to start with a model from previous GASBOR run. Otherwise just press CR.
Symmetry: P1…19 or Pn2 (n=1,..,12) or P23 or P432 or PICO	P1…P19orP12…P122orP23orP432orPICO	P2for GASBORMX, otherwiseP1	Particle symmetry to be enforced. Number of residues given further refers to a single asymmetric unit (monomer).
Number of residues in asymmetric part	integer>0	none	Number of residues within a single asymmetric unit.
Fibonacci grid order	0…18	order that gives number of waters close to the number of dummy residues	Order of the Fibonacci grid to generate dummy waters.
Expected particle shape:<P>rolate,<O>blate, or<U>nknown	P,OorU	U	Constrains particle shape, if it is known to be significantly non-globular (non-spherical). Gives more accurate results in this case.
InExpertmode only:
Number of knots in the curve to fit	11…201	42	Regularized intensity is recomputed to have so many points for fitting.
Radius of the search volume	positive real number	D~max~/2	Radius of the volume in which dummy atoms will be placed. Limits the sampling space.
Histogram penalty weight	positive real number	1.000e-3	Weight of the penalty when histogram of interresidue distances looks different from expected for a protein.
Bond length penalty weight	positive real number	1.000e-2	Penalty for the bond lengths other than 3.8 Å.
Discontiguity penalty weight	positive real number	1.000e-2	Penalty for disconnected dummy residues.
Peripheral penalty weight	positive real number	1.0	Penalty term that ensures compact arrangement of DRs at the beginning. The weight is gradually reduced in the course of simulated annealing.
Contrast of the hydration layer	positive real number	3.000e-2	Contrast of the hydration layer relative to the solvent
Sequence file name	_any filename:_lysozyme.seq	none	Filename with protein sequence to compute the sequence specific dummy residue form factors. Besides otherlimitations, lines in this file must not exceed 256 characters.
Weight:	0	2	Weight I(s) fit according to s^2^
1	as above, with constant for s<MaxPor
2	as above, with average for s<MaxPor
3	weight I(s) proportionaly to s
4	as above, with constant for s<MaxI*s
5	as above, with average for s<MaxI*s
6	compute fit in logarithmic scale
Account for constant background	YesorNo	Yes	Whether constant background should be subtracted when fitting.
Initial scale factor	positive real number	depends on input	Initial scaling factor for fitting experimental data.
Fixing threshold for Rf		0.0	obsolete
Fixing threshold for PenCha		0.0	obsolete
Fixing threshold for PenLen		0.0	obsolete
Initial annealing temperature	positive real number	1.000e-3	Initial temperature for annealing process defines probability of jumping into state of higher pseudo-energy (worse score) on each Monte-Carlo step.
Annealing schedule factor	positive real number<1.0	0.9000	Temperature will be multiplied by this factor after each round of simulated annealing to decrease it.
# of independent atoms to modify	integer>0	1	Number of atoms to reposition on each annealing step.
Max # of iterations at each T	integer≥0	depends on input	Each round of simulated annealing will terminate after at most so many iterations, and temperature will be decreased.
Max # of successes at each T	integer>0	depends on input	Each round of simulated annealing will terminate prematurely after so many successful iterations, and temperature will be decreased.
Min # of successes to continue	integer>1	depends on input	Program will terminate after a round of simulated annealing gives less than so many successes.
Max # of annealing steps	integer>0	100	Maximum number of annealing steps, after which program will always terminate.

Runtime Output

After printing program version number and querying or printing all parameters, GASBOR will display a message that Simulated annealing procedure started and after each round of simulated annealing at new temperature, it will print a report line:

 j:   1 T: 0.100E-02 Suc:  5500 Eva:    11544 CPU:  0.427E+02 SqF: 0.5172
  Rf: 0.08396 His: 26.20 Bnd: 1.302 Dis:0.1593 Per :0.2196

Report header	Columns	Description
j:	4-7	Iteration number.
T:	11-20	Temperature of iteration.
Suc:	27-31	Number of successes at given iteration.
Eva:	38-45	Total number of function evaluations until end of this iteration.
CPU:	52-61	Total CPU time since beginning of run until end of this iteration.
SqF:	68-73	square root of the target function at the end of iteration
Rf:	6-13	R-factor penalty at the end of iteration
His:	19-24	Histogram penalty at the end of iteration
Bnd:	30-35	Bond angle penalty at the end of iteration
Dis:	41-45	Discontiguity penalty at the end of iteration
Per :	53-58	Peripheral penalty at the end of iteration

After run is completed, final \chi ^2^ against data is printed to the output.

gasbor Input Files

The only input file is GNOM output containing both regularized scattering curve and P(r) (for real-space GASBOR.)

gasbor Output Files

After the program is finished, you will get the files:

Filename	Description
<name>.log	log file
<name>.fit	fit to the desmeared and smoothed byGNOMdata (GASBORI)
<name>-i.fit	fits to the desmeared and smoothed byGNOMdata (GASBORMX), where_i_runs from1to thetotal number of curves to fit.
<name>.hst	fit to theGNOMdata in real space (GASBORP)
<name>.fir	fit to the raw experimental data
<name>-i.fir	fits to the raw experimental data (in GASBORMX), where_i_runs from1to thetotal number of curves to fit.
<name>.cif	resulting model incif formatthat can be viewed e.g. withRasMolin thespacefillmode
<name>.pdb	resulting model inPDB-like format(generated if–model-format=pdbcommand line option is used). It can be viewed e.g. withRasMolin thespacefillmode or withMASSHA.

PDB/cif output

PDB-alike output file from GASBOR contains:

Atoms	Meaning
C-lphaatoms (codeCA)	positions of dummy residues
Hatoms	positions of dummy bound waters

Limitations

Problem	Limit	Details
Maximum number of dummy residues and waters	dummy atoms< 8000	As the water shell may be reasonably represented with the ratio of number of residues/number of waters not exceeding 3, the program may currently handle proteins with a total number of residues not exceeding 6000 (i.e. total MM not exceeding ~700 kDa).
Speed	O(dummy atoms^2^)	A GASBOR run on lysozyme (129 residues) on a PIV-2.2 GHz machine required less than an hour of CPU time using GASBORI and less than 20 min using GASBORP. The CPU time grows quadratically with the number of residues so that it may require long times on proteins with high molecular mass.

For large proteins ( > 2000 aminoacids), DAMMIF / DAMMIN is recommended – it will run much faster and give similar results. The influence of the internal structure for large macromolecules is less important and the shape approximation would do a good job.

Examples

Lysozyme

Lysozyme has no symmetry, and 129 residues: Enter P1 symmetry, 129 residues and default answers to all other questions. You may also use command line (Type gasbori –help for batch mode use):

$ gasbori gnlyzfu.out 129

Here is resulting output:

  ***  Ab inito reconstruction of a protein structure    ***
  ***   by a chain-like ensemble of dummy residues       ***
  ***  Please reference: D.I.Svergun, M.V.Petoukhov &    ***
  ***   M.H.J.Koch (2001) Biophys. J. 80, 2946-2953      ***

   Type gasbori --help for batch mode use

  === GASBOR ATSAS 4.0.1 (6378ba7) started on   29-Sep-2023   12:48:23

 Project identifier ..................................... : gnlyzfu
 Project description:
 Initialized random seed as ..................... : 661145759406964600
 Data set title ......................................... : Angular axis n01000.sax             Datafile n10000.sub
 Maximum diameter of the particle ....................... : 50.00
 Radius of gyration ..................................... : 14.33
 Number of GNOM data points ............................. : 230
 Maximum s value [1/angstrom] ........................... : 1.316
 Number of Shannon channels ............................. : 20.94
 Reduced s maximum ...................................... : 1.307
 Reduced number of Shannon channels ..................... : 20.80
 Number of knots in the curve to fit .................... : 42
 Symmetry: P1...19 or Pn2 (n=1,..,12)
 Number of equivalent positions ......................... : 1
  Number of dummy waters ................................ : 90
 Excluded volume per residue ............................ : 28.73
 Radius of the search volume ............................ : 25.00
 Histogram penalty weight ............................... : 1.000E-03
 Bond length penalty weight ............................. : 1.000E-02
 Discontiguity penalty weight ........................... : 1.000E-02
 Peripheral penalty weight .............................. : 1.000
 Contrast of the hydration layer ........................ : 3.000E-02
  Computation of the initial intensity ...
 Histogram penalty value ................................ : 40.11
 Bond length penalty value .............................. : 2.402
 Initial DRM # of graphs ................................ : 60
 Discontiguity   value .................................. : 1.099
 Peripheral penalty value ............................... : 0.2496
 Weight: 0-2 = s^2, 3-5 = s, 6 = log .................... : 2
 *** Accounting for constant background ***
 Initial scale factor ................................... : 1.092E-04
 Constant background subtracted ......................... : -0.4002
 Initial R^2 factor ..................................... : 0.1164
 Initial R   factor ..................................... : 0.3412
 Initial penalty ........................................ : 0.3247
 Initial fVal ........................................... : 0.4411
 R-factor fixing threshold .............................. : 0.0
 Fixing threshold PenCha ................................ : 0.0
 Fixing threshold PenLen ................................ : 0.0
 Initial annealing temperature .......................... : 1.000E-03
 Annealing schedule factor .............................. : 0.9000
 # of independent atoms to modify ....................... : 1
 Max # of iterations at each T .......................... : 55000
 Max # of successes at each T ........................... : 5500
 Min # of successes to continue ......................... : 55
 Max # of annealing steps ............................... : 100
  ====  Simulated annealing procedure started  ====
 j:   1 T: 0.100E-02 Suc:  5500 Eva:    11278 CPU:  0.106E+01 SqF: 0.5132
  Rf: 0.09491 His: 25.78 Bnd: 1.398 Dis:0.1870 Per :0.2127
_..._
 j:  36 T: 0.250E-04 Suc:    55  j:  36 T: 0.250E-04 Suc:    53 Eva:  1427584 CPU:  0.135E+03 SqF: 0.0912
  Rf: 0.03409 His:  6.26 Bnd: 0.065 Dis:0.0000 Per :0.3664

 Final Chi^2 against raw data ........................... : 1.248

  === GASBOR ATSAS 4.0.1 (6378ba7) finished on   29-Sep-2023   12:44:39

Transketolase

Transketolase is homodimer in solution, and each monomer has 680 residues, giving a total of 1360 residues: Enter P2 for symmetry, 680 for residues and default answers to all other questions.

  ***  Ab inito reconstruction of a protein structure    ***
  ***   by a chain-like ensemble of dummy residues       ***
  ***  Please reference: D.I.Svergun, M.V.Petoukhov &    ***
  ***   M.H.J.Koch (2001) Biophys. J. 80, 2946-2953      ***

   Type gasbori --help for batch mode use

  === GASBOR ATSAS 4.0.1 (6378ba7) started on   29-Sep-2023   12:56:50
  
 Computation mode (User or Expert) ...... <         User >:
 Log file name .......................... <         .log >: **log**
 Input data, GNOM output file name ...... <         .out >: **1trk.out**
 Project identificator .................................. : log
 Enter project description .............. : **project**
 Random sequence initialized from ....................... : 164228
  ** Information read from the GNOM file **
 Data set title:    Transketolase collated from n85, o14+o16   6-11-98
 Raw data file name:  trkexp.dat
 Maximum diameter of the particle ....................... : 12.00
  Solution at Alpha =   .164E+01   Rg :   .336E+01   I(0) :    .190E+03
 Radius of gyration ..................................... : 3.360
 Number of GNOM data points ............................. : 283
 Angular units in the input file :
 4*pi*sin(theta)/lambda [1/angstrom] (1)
 4*pi*sin(theta)/lambda [1/nm      ] (2)  <            2 >: **2**
 Angular units multiplied by ............................ : 0.1000
 Maximum diameter divided by ............................ : 0.1000
 Maximum s value [1/angstrom] ........................... : 0.3418
 Number of Shannon channels ............................. : 13.06
 Portion of the curve to be fitted ...... <        1.000 >:
 Number of knots in the curve to fit .................... : 26
 Initial DRM (CR for random) ............ <         .pdb >:
 Symmetry: P1...19 or Pn2 (n=1,..,12)
 or P23 or P432 or PICO ................. <           P1 >: **P2**
 Number of equivalent positions ......................... : 2
 Number of residues in asymmetric part .. <          517 >: **680**
 Fibonacci grid order ................... <           15 >:
 Number of dummy waters ................................ : 988
 Excluded volume per residue ............................ : 28.73
 Radius of the search volume ............................ : 60.00
 Histogram penalty weight ............................... : 1.000e-3
 Bond length penalty weight ............................. : 1.000e-2
 Discontiguity penalty weight ........................... : 1.000e-2
 Peripheral penalty weight .............................. : 1.000
 Expected particle shape: <P>rolate, <O>blate,
  or <U>nknown .......................... <      Unknown >:
 Contrast of the hydration layer ........................ : 3.000e-2
  Computation of the initial intensity ...
 Histogram penalty value ................................ : 37.38
 Bond length penalty value .............................. : 1.604
 Initial DRM # of graphs ................................ : 708
 Discontiguity   value .................................. : 2.191
 Peripheral penalty value ............................... : 0.2647
 Weight: 0-2 = s^2, 3-5 = s, 6 = log .................... : 2
 *** Accounting for constant background ***
 Initial scale factor ................................... : 5.042e-7
 Constant background subtracted ......................... : 0.3339
 Initial R^2 factor ..................................... : 3.837e-2
 Initial R   factor ..................................... : 0.1959
 Initial penalty ........................................ : 0.3400
 Initial fVal ........................................... : 0.3784
 R-factor fixing threshold .............................. : 0.0
 Fixing threshold PenCha ................................ : 0.0
 Fixing threshold PenLen ................................ : 0.0
 Initial annealing temperature .......................... : 1.000e-3
 Annealing schedule factor .............................. : 0.9000
 # of independent atoms to modify ....................... : 1
 Max # of iterations at each T .......................... : 130000
 Max # of successes at each T ........................... : 13000
 Min # of successes to continue ......................... : 130
 Max # of annealing steps ............................... : 100
  ====  Simulated annealing procedure started  ====
 j:   1 T: 0.100E-02 Suc: 13000 Eva:    14975 CPU:  0.272E+02 SqF: 0.5531
  Rf: 0.11900 His: 36.59 Bnd: 2.213 Dis:0.3588 Per :0.2294
_..._
 j:  56 T: 0.304E-05 Suc:    85 Eva:  3737295 CPU:  0.680E+04 SqF: 0.0797
  Rf: 0.02350 His:  5.37 Bnd: 0.044 Dis:0.0000 Per :0.3197

 Final Chi^2 against raw data ........................... : 1.774

  === GASBOR ATSAS 4.0.1 (6378ba7) finished on   29-Sep-2023   14:57:15

Lysozyme in Expert mode with sequence file

Lysozyme example with sequence-specific form-factors of dummy residues. Enter E for Expert mode, P1 symmetry, 129 residues, lyz.seq for the sequence and default answers to all other questions.

  ***  Ab inito reconstruction of a protein structure    ***
  ***   by a chain-like ensemble of dummy residues       ***
  ***  Please reference: D.I.Svergun, M.V.Petoukhov &    ***
  ***   M.H.J.Koch (2001) Biophys. J. 80, 2946-2953      ***

   Type gasbori --help for batch mode use

  === GASBOR ATSAS 4.0.1 (8aa369f3b) started on   02-Oct-2023   13:55:24

 Computation mode (User or Expert) ...... <         User >: **E**
 Log file name .......................... <         .log >: **lyzseq**
 Input data, GNOM output file name ...... <         .out >: **gnlyzfu**
 Project identifier ..................................... : lyzseq
 Enter project description .............. : **use sequence**
Initial random seed? (default: use current time) ..................... :
 Warning: initialising the random seed when it has already been initialised
 Previous seed:     39884949516326408
 New seed:          39888779342845448
 Initialized random seed as ..................... : 39888779342845448
 Data set title ......................................... : Angular axis n01000.sax             Datafile n10000.sub
 Maximum diameter of the particle ....................... : 50.00
 Radius of gyration ..................................... : 14.33
 Number of GNOM data points ............................. : 230
 Angular units in the input file :
 4*pi*sin(theta)/lambda [1/angstrom] (1)
 4*pi*sin(theta)/lambda [1/nm      ] (2)  <            1 >:
 Maximum s value [1/angstrom] ........................... : 1.316
 Number of Shannon channels ............................. : 20.94
 Portion of the curve to be fitted ...... <        1.000 >:
 Reduced s maximum ...................................... : 1.307
 Reduced number of Shannon channels ..................... : 20.80
 Number of knots in the curve to fit .... <           42 >:
 Initial DRM (CR for random) ............ <         .pdb >:
 Symmetry: P1...19 or Pn2 (n=1,..,12)
 or P23 or P432 or PICO ................. <           P1 >: **P1**
 Number of equivalent positions ......................... : 1
 Number of residues in asymmetric part .. <           80 >: **129**
 Fibonacci grid order ................... <           10 >:
  Number of dummy waters ................................ : 90
 Excluded volume per residue ............................ : 28.73
 Radius of the search volume ............ <        25.00 >:
 Histogram penalty weight ............... <    1.0000E-3 >:
 Bond length penalty weight ............. <    1.0000E-2 >:
 Discontiguity penalty weight ........... <    1.0000E-2 >:
 Peripheral penalty weight .............. <        1.000 >:
 Expected particle shape: <P>rolate, <O>blate,
  or <U>nknown .......................... <      Unknown >:
 Contrast of the hydration layer ........ <    3.0000E-2 >:
 Seqence file name, CR for none ......... <         .seq >: **lyz**
 Sequence file name ..................................... : lyz.seq
  Computation of the initial intensity ...
 Histogram penalty value ................................ : 27.84
 Bond length penalty value .............................. : 1.772
 Initial DRM # of graphs ................................ : 65
 Discontiguity   value .................................. : 2.152
 Peripheral penalty value ............................... : 0.2892
Weight: 0=s^2,1=const at s<MaxPor,2=aver
Weight: 3=s  ,4=const at s<MaxI*s,5=aver
 Weight: 6=logarithmic scale ............ <            2 >:
 Account for constant background [ Y / N ] <          Yes >:
 *** Accounting for constant background ***
 Initial scale factor ................... <    9.9872E-5 >:
 Constant background subtracted ......................... : -0.4946
 Initial R^2 factor ..................................... : 0.1717
 Initial R   factor ..................................... : 0.4144
 Initial penalty ........................................ : 0.3563
 Initial fVal ........................................... : 0.5280
 Fixing threshold for Rf ................ <        0.000 >:
 Fixing threshold for PenCha ............ <        0.000 >:
 Fixing threshold for PenLen ............ <        0.000 >:
 Initial annealing temperature .......... <    1.0000E-3 >:
 Annealing schedule factor .............. <       0.9000 >:
 # of independent atoms to modify ....... <            1 >:
 Max # of iterations at each T .......... <        55000 >:
 Max # of successes at each T ........... <         5500 >:
 Min # of successes to continue ......... <           55 >:
 Max # of annealing steps ............... <          100 >:
  ====  Simulated annealing procedure started  ====
 j:   1 T: 0.100E-02 Suc:  5500 Eva:    10277 CPU:  0.969E+00 SqF: 0.5257
  Rf: 0.11500 His: 29.47 Bnd: 1.951 Dis:0.0315 Per :0.2139
_..._
 j:  37 T: 0.225E-04 Suc:    36 Eva:  1431936 CPU:  0.134E+03 SqF: 0.0943
  Rf: 0.03583 His:  6.50 Bnd: 0.087 Dis:0.0000 Per :0.4718

 Final Chi^2 against raw data ........................... : 1.335

  === GASBOR ATSAS 4.0.1 (8aa369f3b) finished on   02-Oct-2023   13:58:36

Gasbormx on concentration series of Tetanus toxin

There are three curves available on Tetanus toxin: one corresponds to pure monomer, the other two are from monomer-dimer equilibrium with unknown volume fractions. In this gasbormx example all three curves are fitted simultaneously, while keeping the volume fraction of the monomer fixed to 1 for the monoimer curve and varying monomer and dimer volume fractions for the other two. The overall P2 symmetry is used and 451 residues per monomer are generated.

  ***  Ab inito reconstruction of a protein structure    ***
  ***  by a chain-like ensemble of dummy residues (mix)  ***
  ***  Takes into account oligomer-monomer equilibrium   ***
  ***  Please reference: D.I.Svergun, M.V.Petoukhov &    ***
  ***   M.H.J.Koch (2001) Biophys. J. 80, 2946-2953      ***

   Type gasbormx --help for batch mode use

  === GASBOR ATSAS 4.0.1 (6378ba7) started on   01-Oct-2023   16:22:34

 Computation mode (User or Expert) ...... <         User >:
 Log file name .......................... <         .log >: **tetomx1**
 Project identifier ..................................... : tetomx1
 Enter project description .............. : **3 curves**
 Warning: initialising the random seed when it has already been initialised
 Previous seed:     27016039586466748
 New seed:          27020856437574588
 Initialized random seed as ..................... : 27020856437574588
 Total number of curves to fit .......... <            1 >: **3**
 Number of knots on the master grid ..................... : 101
 Curve # ................................................ : 1
 Input data, GNOM output file name ...... <         .out >: **hcm_mer**
 Data set title
 Maximum diameter of the particle ....................... : 10.05
 Radius of gyration ..................................... : 2.938
 Number of GNOM data points ............................. : 591
 Angular units in the input file :
 4*pi*sin(theta)/lambda [1/angstrom] (1)
 4*pi*sin(theta)/lambda [1/nm      ] (2)  <            2 >:
 Angular units multiplied by ............................ : 0.1000
 Maximum diameter divided by ............................ : 0.1000
 Maximum s value [1/angstrom] ........................... : 0.2691
 Number of Shannon channels ............................. : 8.608
 Portion of the curve to be fitted ...... <        1.000 >:
 Reduced s maximum ...................................... : 0.2684
 Reduced number of Shannon channels ..................... : 8.585
 Volume fraction of monomer (if known) .. <       -1.000 >: **1**
 Curve # ................................................ : 2
 Input data, GNOM output file name ...... <         .out >: **hcp_a46c**
 Data set title
 Maximum diameter of the particle ....................... : 13.00
 Radius of gyration ..................................... : 3.907
 Number of GNOM data points ............................. : 941
 Angular units in the input file :
 4*pi*sin(theta)/lambda [1/angstrom] (1)
 4*pi*sin(theta)/lambda [1/nm      ] (2)  <            2 >:
 Angular units multiplied by ............................ : 0.1000
 Maximum diameter divided by ............................ : 0.1000
 Maximum s value [1/angstrom] ........................... : 0.3384
 Number of Shannon channels ............................. : 14.00
 Portion of the curve to be fitted ...... <        1.000 >:
 Reduced s maximum ...................................... : 0.3381
 Reduced number of Shannon channels ..................... : 13.99
 Volume fraction of monomer (if known) .. <       -1.000 >:
 Curve # ................................................ : 3
 Input data, GNOM output file name ...... <         .out >: **hcp_a48c**
 Data set title
 Maximum diameter of the particle ....................... : 15.00
 Radius of gyration ..................................... : 4.393
 Number of GNOM data points ............................. : 944
 Angular units in the input file :
 4*pi*sin(theta)/lambda [1/angstrom] (1)
 4*pi*sin(theta)/lambda [1/nm      ] (2)  <            2 >:
 Angular units multiplied by ............................ : 0.1000
 Maximum diameter divided by ............................ : 0.1000
 Maximum s value [1/angstrom] ........................... : 0.3384
 Number of Shannon channels ............................. : 16.16
 Portion of the curve to be fitted ...... <        1.000 >:
 Reduced s maximum ...................................... : 0.3381
 Reduced number of Shannon channels ..................... : 16.14
 Volume fraction of monomer (if known) .. <       -1.000 >:
 Initial DRM (CR for random) ............ <         .pdb >:
 Symmetry: P2...9 or Pn2 (n=2,..,9)
 or P23 or P432 or PICO ................. <           P2 >:**P2**
 Number of equivalent positions ......................... : 2
 Number of residues in asymmetric part .. <         1156 >: **451**
 Fibonacci grid order ................... <           14 >:
 Number of dummy waters ................................. : 611
 Excluded volume per residue ............................ : 28.73
 Radius of the search volume ............................ : 75.00
 Histogram penalty weight ............................... : 1.000E-03
 Bond length penalty weight ............................. : 1.000E-02
 Discontiguity penalty weight ........................... : 1.000E-02
 Peripheral penalty weight .............................. : 5.000E-02
 Expected particle shape: <P>rolate, <O>blate,
  or <U>nknown .......................... <      Unknown >:
 Contrast of the hydration layer ........................ : 3.000E-02
  Computation of the initial intensity ...
 Histogram penalty value ................................ : 32.79
 Bond length penalty value .............................. : 0.6398
 Initial DRM # of graphs ................................ : 731
 Discontiguity   value .................................. : 4.725
 Peripheral penalty value ............................... : 0.2862
 Weight: 0-2 = s^2, 3-5 = s, 6 = log .................... : 2
 *** Accounting for constant background ***
 Constant background subtracted ......................... : -8.012E-04
 Initial R^2 factor ..................................... : 0.5078
 Initial R   factor ..................................... : 0.7126
 Volume fraction, monomer ............................... : 1.000
 Constant background subtracted ......................... : -0.1363
 Initial R^2 factor ..................................... : 7.185
 Initial R   factor ..................................... : 2.681
 Volume fraction, monomer ............................... : 1.000
 Constant background subtracted ......................... : -0.5360
 Initial R^2 factor ..................................... : 7.029
 Initial R   factor ..................................... : 2.651
 Initial penalty ........................................ : 0.1007
 Initial fVal ........................................... : 14.82
 Initial annealing temperature .......................... : 0.100
 Annealing schedule factor .............................. : 0.9000
 # of independent atoms to modify ....................... : 1
 Max # of iterations at each T .......................... : 105000
 Max # of successes at each T ........................... : 10500
 Min # of successes to continue ......................... : 105
 Max # of annealing steps ............................... : 100
  ====  Simulated annealing procedure started  ====
 j:   1 T: 0.100E+00 Suc: 10500 Eva:    10921 CPU:  0.311E+02 SqF: 0.4654
  Rf: 0.35014 His: 36.75 Bnd: 2.707 Dis:2.0684 Per :0.1894
_..._
 j:  96 T: 0.450E-05 Suc:    98 Eva:  3542664 CPU:  0.764E+04 SqF: 0.0942
  Rf: 0.05956 His:  4.96 Bnd: 0.038 Dis:0.0000 Per :0.1477

 Final Chi^2 against raw data ........................... : 1.669
 Final Chi^2 against raw data ........................... : 0.9622
 Final Chi^2 against raw data ........................... : 1.172

  === GASBOR ATSAS 4.0.1 (6378ba7) started on   01-Oct-2023   18:32:46

References

• Svergun, D.I., Petoukhov, M.V.&Koch, M.H.J. (2001) Determination of domain structure of proteins from X-ray solution scattering.Biophys. J.80, 2946-2953.
• Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G., Gajda, M., Gorba, C., Mertens, H.D.T., Konarev, P.V. and Svergun, D.I. (2012)New developments in the ATSAS program package for small-angle scattering data analysis.J. Appl. Cryst.45, 342-350(c)International Union of CrystallographyDOI