GAJOE no PDB output in file / CaCa_dist file doesnt look right

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)
Post Reply
Message
Author
nmeri
Member
Posts: 4
Joined: 2018.04.06 01:10

GAJOE no PDB output in file / CaCa_dist file doesnt look right

#1 Post by nmeri » 2018.07.14 02:06

Hi,
I am running GAJOE on a pool of 10k pdb files I generated with TraDES. The program seems to run smoothly, I get no errors, however output seems to be strange.

First, here is the log file I get

Code: Select all

[size=85]Experimental data file name ............................ : 280_h_A4_1.mccd.dat
 -------------------------------------------
 -- Pool(s)
 Pool of PDBs, directory ................................ : TraDES_pool/
 Intensities file name .................................. : junXXX.eom
 -------------------------------------------
 -- 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? .......................... : Y
 Curve repetition in the ensemble allowed? .............. : Y
 Number of times you want the genetic algorithm repeated (min. 1): 100
 -------------------------------------------
 -- Number of theoretical curves :        10000
 -------------------------------------------
 Start:  Fri Jul 13 13:53:30 2018
 End:    Fri Jul 13 15:27:42 2018
 -------------------------------------------
 -- Chi^2 :  1.721
 -------------------------------------------
 -- Rflex (random) / Rsigma: ~ 82.93% (~ 83.17%) / 1.55
 -------------------------------------------
 -- Constant subtracted :  0.787
 -------------------------------------------
 -- Files created:
 Fit to the experimental data (in 1/angstrom) ........... : profiles_001_1.fit
 Radius of gyration distribution (in angstrom) .......... : Rg_distr_001_1.txt
 Max Dimensions distribution (in angstrom) .............. : Size_distr_001_1.txt
 Ca(N)-Ca(C) distances distribution (in angstrom) ....... : CaCa_distr_001_1.txt
 Volume distribution (in angstrom) ...................... : Volume_distr_001_1.txt
 -------------------------------------------
 -- PDB models in the folder "GA001/curve_1/pdb":
  #  Filename           Rg       Dmax     Fraction        

  1) TraDES_pool/   46.94     155.91    ~0.061.00  17
  2) TraDES_pool/  37.12     113.86    ~0.061.00  17
  3) TraDES_pool/   61.85     181.54    ~0.061.00  17
  4) TraDES_pool/  78.44     244.20    ~0.061.00  17
  5) TraDES_pool/   57.76     186.44    ~0.061.00  17
  6) TraDES_pool/  37.31     120.70    ~0.061.00  17
  7) TraDES_pool/   35.52     116.47    ~0.061.00  17
  8) TraDES_pool/   50.95     177.73    ~0.061.00  17
  9) TraDES_pool/   46.47     140.48    ~0.061.00  17
 10) TraDES_pool/   56.18     182.62    ~0.061.00  17
 11) TraDES_pool/   45.02     139.65    ~0.061.00  17
 12) TraDES_pool/  51.12     159.91    ~0.061.00  17
 13) TraDES_pool/   71.72     224.73    ~0.061.00  17
 14) TraDES_pool/  49.90     161.59    ~0.061.00  17
 15) TraDES_pool/   75.05     266.38    ~0.061.00  17
 16) TraDES_pool/   48.99     170.59    ~0.061.00  17
 17) TraDES_pool/   50.12     164.03    ~0.061.00  17

 Final ensemble :           52.97     170.99[/size]

1 - It looks like I had to get 17 pdbs in pdbs directory but there is none. I wonder if I miss something extremely trivial but I tried running this several times and I get no structures.
2 - I get a good fit (judged from profiles.fit), reasonable Rg_distr etc. One thing that does not look ok (at least when I compared to my previous runs with RANCH output) is CaCa_dist. Here it is:

Code: Select all

 Ense  Average  Ca(N)-Ca(C) distance =   0.00
 Ense  Average  Ca(N)-Ca(C) distance =   0.00
 Pool  Average  Ca(N)-Ca(C) distance =   0.00
 Pool Histogram Ca(N)-Ca(C) distance =   0.00
    Distance    Pool freq.    Sel. freq.
       -0.00  0.0000000000  0.0000000000
       -0.00  0.2000000000  0.2000000000
        0.00  0.2000000000  0.2000000000
        0.00  0.2000000000  0.2000000000
        0.00  0.2000000000  0.2000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.00  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
        0.01  0.0000000000  0.0000000000
This really puzzles me. In my opinion, GA does a good job considering there are no errors and Rgs and fit profile is very nice but the program seems to fail at some point. I'd be glad to provide additional details if needed on this run. Thank you so much!

Post Reply