Reg : Gajoe run an external pool (own pool) results negative chi2 Value

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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vas2201
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Reg : Gajoe run an external pool (own pool) results negative chi2 Value

#1 Post by vas2201 » 2018.08.28 20:31

Hello,

I am running GAJOE on the external pool that I created from amber MD trajectory! I used VMD script to write the PDB files. I ran the Gajoe -p to select the conformational ensemble which agrees with SAX data.
Looks like GAJOE run was fine. but the log file was showing negative chi2 value and it also created profiles_001_1.fit and it doesn't contain any values to create the plot.
Could you please let me know where I am doing wrong or any error/ bug associated with Gajoe ?.
Thank you!

profiles_001_1.fit output !

CYCLE: 28 Chi^2:-1.000 GENER.:1000 ENSEMBLES: 50 CURVES: 5



logfile_001_1.log


Copyright (c) ATSAS Team *******
******* EMBL, Hamburg Outstation, 2007 - 2014 *******
******* *******
******* For doubts/questions please visit SAXIER forum: *******
******* http://www.saxier.org/forum/viewforum.php?f=10 *******
******* *******
******* In case of bugs please refer to: *******
******* G. Tria, D.I. Svergun, EMBL BioSAXS group *******
******* atsas@embl-hamburg.de *******
******* ------------------------------------------------------ *******

Experimental data file name
-------------------------------------------
-- Pool(s)
Pool of PDBs, directory ................................ : ./
Intensities file name .................................. : junXXX.int
-------------------------------------------
-- Standard Mode
Maximum number of curves per ensemble (min. 1, max. 50) : 20
Minimum number of curves per ensemble (min. 1) ......... : 5
Constant subtraction allowed? .......................... : N
Curve repetition in the ensemble allowed? .............. : Y
Number of times you want the genetic algorithm repeated (min. 1): 100
-------------------------------------------
-- Number of theoretical curves : 3118
-------------------------------------------
Start: Thu Aug 23 14:13:57 2018
End: Thu Aug 23 14:37:35 2018
-------------------------------------------
-- Chi^2 : -1.000
-------------------------------------------
-- Rflex (random) / Rsigma: ~ 86.51% (~ 85.48%) / 1.00
-------------------------------------------
-- Constant subtracted : 0.000
-------------------------------------------
-- Files created:
Fit to the experimental data (in Å-1) ................. : profiles_001_1.fit
Radius of gyration distribution (in Å) ................ : Rg_distr_001_1.dat
Max Dimensions distribution (in Å) .................... : Size_distr_001_1.dat
Ca(N)-Ca(C) distances distribution (in Å) ............. : CaCa_distr_001_1.dat
-------------------------------------------
-- PDB models in the folder "GA001/curve_1/pdb":
# Filename Rg Dmax Fraction

1) ./aufr12_1166.pdb 23.50 74.29 ~0.20
2) ./aufr12_1752.pdb 21.04 62.71 ~0.20
3) ./aufr12_1980.pdb 22.06 71.95 ~0.20
4) ./aufr12_313.pdb 23.42 70.65 ~0.20
5) ./aufr12_354.pdb 22.69 70.70 ~0.20

Final ensemble : 22.54 70.06

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