Member Site › Forums › Rosetta 3 › Rosetta 3 – General › What is a “silent file”?
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September 22, 2014 at 9:43 am #1995Anonymous
Dear Sir or Madam,
I tried to look at explanation athttps://www.rosettacommons.org/docs/latest/input-options.html
but still could not figure out the meaning of a “silent file”. Can I ask what is it used for? Why is it called “silent”?
The following is part of the beginning content copied from “cluster_all.out” by following “modeling_instructions.pdf” in “Homology or Loop Modelling”.
http://www.meilerlab.org/index.php/jobs/resourcesAs I understand, it should contain multiple PDB information but I am really confused about the characters.
Thank you very much.
Yours sincerely
ChengSEQUENCE: MKIVYWSGTGNTEKMAELIAKGIIESGKDVNTINVSDVNIDELLNEDILILGCSAMGDEVLEESEFEPFIEEISTKISGKKVALFGSYGWGDGKWMRDFEERMNGYGCVVVETPLIVQNEPDEAEQDCIEFGKKIANI
SCORE: score fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref aln_ident aln_len aln_perc brlx_corerms brlx_irms brlx_looprms brlx_rms cen_irms cen_loopcarms cen_looprms cen_rms corelen corerms final_looprelax_score irms loopcarms looprms maxsub nres rms silent_score time aln_id template description
SCORE: -230.424 -488.562 70.107 224.909 1.393 0.662 -13.804 -27.221 -37.339 -9.520 -7.676 0.000 0.000 0.000 0.000 -1.761 13.293 85.437 -12.242 -28.100 0.304 137.000 0.993 2.553 3.354 50.987 2.668 3.354 50.983 51.009 2.670 127.000 2.734 -230.426 3.828 51.026 51.172 138.000 138.000 2.792 -230.426 112.000 1F4PA 1f4pA.pdb S_1F4PA_0001
REMARK BINARY SILENTFILE
REMARK query_alignment 2foxA
REMARK template_alignment 1f4pA
REMARK BINARY SILENTFILE
ANNOTATED_SEQUENCE: M[MET_p:NtermProteinFull]KIVYWSGTGNTEKMAELIAKGIIESGKDVNTINVSDVNIDELLNEDILILGCSAMGDEVLEESEFEPFIEEISTKISGKKVALFGSYGWGDGKWMRDFEERMNGYGCVVVETPLIVQNEPDEAEQDCIEFGKKIANI[ILE_p:CtermProteinFull] S_1F4PA_0001
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LtiLVAPQAn+LTtIMQ6mARATo5iAMLhsKQ1EjgAPk+nBsTLdLQQw1kAnA9nBcv/qNQaDd0/6HNCBcxnPLQlijs/GkTbBso7HOQj0As/OUUYCsR64OQ+Lml/+qjdA8MMCQQyF1k/yP9jC8ViwQQ6Auc/eyE0AMqcWRQ15/b/qgrECs1YtRQRUjN/2eEQC82NBTQebvZAz6ls+r0mEOQDMySA/XZYAs7RjIQoS1u/mZU5Bcy48JQ4Old/CriOA8ADsKQIjbx/mL2wC8mEYNQLH8l/y8m0+LHVfPQ5Vgk/GZmFD802CRQjm/R/uVkCA8AcGSQfvzE/6twvBs4FmTQ S_1F4PA_0001
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L2V018YIkBF804FEQYAHo/Mhr8EcaGMBQWnyu/QZnkE8NJtAQT7LJAdSpcE84GaBQXxTo/4s9GFsbkw2PLyou/8nzeFcTsO3Px/N+/AtznFcn7g/P6+El/E65oFMhn6hv5GPO/yAPJFsHMLCQmR0BA1N5CFMwTYDQdnz++0bDDFMMtDkP3kLDApGZ/EM3vKyP3Cfo/4Iz4Fc4fSlvrzvU/kivgF84ZJ3v S_1F4PA_0001
L0Idx+42GZEM3KA/P2FV3+oM0BEcysd+P9v5H/s3HwDs+1wEQsniq/M2PQD8CMZFQmyRW/OMKxDMtWa5P5old/yFs/Dst9ajvMUGU/CQgAD8Znk5PnFL+++HsgEsKbg9PV/Op/cej5Ds/Gs5Pyzw2/+iY8Dsiw79P+Ppf/WvMPEcDySkvNJR3/uDD0CMdc8zPq7RP/+GX1CMD/5AQcRGR9gJR1C8W2FyP S_1F4PA_0001
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September 22, 2014 at 2:54 pm #10288Anonymous
https://www.rosettacommons.org/docs/latest/silent-file.html
Silent files are Rosetta-only file formats used for concatenated storage of structures. Most computers’ file systems perform poorly if you try to put 10,000 PDB files totaling a few GB of disk space into one directory, but they perform great for one many-GB huge file in the directory. This is what silent files do: concatenate structures into one big file. Another way to look at it is as a really poorly written relational database (written long before Rosetta supported actual relational databases).
The “letters and numbers” are because this is a binary-type silent file, which means each of those lines is a binary representation of one residue of your protein. The binary gets interpreted as ASCII and then into characters from there, but it’s not meant to be human-readable.
If you need an input to Rosetta, silent files work fine, using -in:file:silent. If you need the PDB structure, use the extract_pdbs application, which will just dump all your structures into pdb format. The tag option allows you to get only a few at a time.
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September 22, 2014 at 3:13 pm #10290Anonymous
Hi Smlewis,
Thank you very much. I got it. At least I know what it is used for and why it looks like that.Yours sincerely
Cheng
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