combine silent.out file

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    • July 22, 2016 at 12:22 pm #2470
      Anonymous

        greetings, 

                     am tried to combine silent_1.out to silent_23.out  by using following commands 

        PATH/rosetta_bin_linux_2016.17.58663_bundle/main/source/bin/combine_silent.mpi.linuxgccrelease

        -in:file:silent silent_1.out silent_2.out silent_3.out  silent_4.out silent_5.out silent_6.out  silent_7.out silent_8.out  silent_9.out  silent_10.out  silent_11.out  silent_12.out  silent_13.out  silent_14.out  silent_15.out  silent_16.out  silent_17.out  silent_18.out  silent_19.out  silent_20.out  silent_21.out  silent_22.out silent_23.out  

        -in:file:silent_struct_type binary

        -out:file:silent_struct_type binary

        -out:file:silent  silent.out 

        got following silent.out  (F_00000006) numerous time why? and after pdb extracted, found six time the same F_00000006 _1 to _6  file ?

        EXPECTING YOUR ANWERS 

        THANK YOU 

        SEQUENCE: LPHEMSPALHRKISVQYGDAFHPRPFCMRRVKEMDAYGMVSPFARRPSVNSDLKYIKAKVLREGQARERDKCTIQ

        SCORE:     score     fa_atr     fa_rep     fa_sol    fa_intra_rep    fa_elec    pro_close    hbond_sr_bb    hbond_lr_bb    hbond_bb_sc    hbon

        d_sc    dslf_fa13       rama      omega     fa_dun    p_aa_pp    yhh_planarity        ref         co    Filter_Stage2_aBefore    Filter_Stage2

        _bQuarter    Filter_Stage2_cHalf    Filter_Stage2_dEnd    clashes_bb    clashes_total    silent_score    time description

        REMARK BINARY SILENTFILE

        SCORE:   364.490   -238.385    337.753    141.980           3.047     -5.128        2.032        -10.709         -0.037         -2.144      -0

        .911        0.000     -7.370     11.154    120.696     -0.529            0.013     -3.909     16.937                    0.000                 

            0.000                  0.000                 0.000         0.000            0.000         347.553 272.000  F_00000006

        ANNOTATED_SEQUENCE: L[LEU:NtermProteinFull]PHEMSPALH[HIS_D]RKISVQYGDAFHPRPFCMRRVKEMDAYGMVSPFARRPSVNSDLKYIKAKVLREGQARERDKCTIQ[GLN:CtermProteinF

        ull] F_00000006

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      • July 22, 2016 at 2:31 pm #11754
        Anonymous

          Your question isn’t clear to me, but I don’t think you’re having a problem combining silent files, I think you’re either worried that the model IDs are similar (not a problem) or that the model data is identical (a fixable problem).

           

          If the question is “why does F_000006 occur repeatedly in the inputs and become F_000006_01, F_000006_02” – that’s the way it’s supposed to work.  The separate silent files don’t know about each other to number themselves uniquely.

           

          If the problem is “I have many copies of a file named “F_000006″, with or without the _01, _02 decoration, and all of those files produce identical coordinates”, then the problem is that in your original run, you had overlapping random number seeds.  There are dozens of other posts on this forum explaining the need for unique random number seeds.  Briefly, if you run Rosetta with identical inputs, you’ll get identical outputs, because computers are deterministic.  The random number seed is an input meant to be always different to break this identical output problem by tweaking the random number generator.  The random number seed is taken from an operating system process; sometimes it’s different for each Rosetta invocation but sometimes it’s just the POSIX timestamp, so many processes started simultaneously get the same random number seed.  If that’s what happened, re-do your runs with -constant_seed -jran #####, where ##### is a different value for each invocation.

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