extract silent error – tag mismatch

[Anonymous]

Dear all,

I have been trying to extract PDBs from silent file and keep getting this error:

core.init: command: /opt/rosetta3.3/rosetta_source/bin/extract_pdbs.linuxgccrelease -in:file:silent silent.out -database /opt/rosetta3.3/rosetta_database/
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-20988320 seed_offset=0 real_seed=-20988320
core.init.random: RandomGenerator:init: Normal mode, seed=-20988320 RG_type=mt19937
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types
core.io.silent: Reading all structures from silent.out
Input failed: tag mismatch JUMP_CLONES
Input failed: tag mismatch BB_FOLLOWS
Input failed: tag mismatch CHI_FOLLOWS
Input failed: tag mismatch JUMP_FOLLOWS
Input failed: tag mismatch DOFS
Input failed: tag mismatch SCORE_MULTIPLY
Segmentation fault (core dumped)

can anyone tell me what could be the reason for this problem?

thanks..

[Anonymous]

One possibility is that you’re trying to read a silent file produced with a later version of Rosetta. The silent file format has had some additions over the years, so older versions of Rosetta may not be able to read silent files produced with later versions. (We try to be backward compatible, so old silent files should be readable by newer versions, but sometimes that breaks too.)

The other possibility is that you have a corrupt silent file. Try using the flag “-silent_read_through_errors”. This will try to skip structures with errors.

If neither of these two works/applies, we’d likely have to take a closer look at your silent file.

[Anonymous]

yes I am using symmetry. I tried providing symm file, again it gave same error.
posting silent file part here:
SEQUENCE: MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGIMQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGIXX
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 Filter_Stage2_aBefore Filter_Stage2_bQuarter Filter_Stage2_cHalf Filter_Stage2_dEnd loop_chain_score loop_overlap_score loop_total_score loop_vdw_score looprms prefa_centroid_score time description
SCORE: -318.614 -704.696 96.701 353.708 1.771 0.506 -12.745 -39.177 -17.803 -25.208 -22.970 0.000 0.000 0.000 0.000 -18.256 14.310 115.789 -18.106 -42.440 0.000 0.000 0.000 0.000 -1.000 -1.000 -1.000 -1.000 -1.000 5.306 360.000 S_00001
REMARK BINARY SILENTFILE
FOLD_TREE EDGE 203 97 1 EDGE 203 204 3 EDGE 204 198 2 EDGE 198 102 -1 EDGE 198 202 -1 EDGE 97 1 -1 EDGE 97 101 -1 S_00001
RT 0.807551 -0.566465 0.164254 -0.228262 -0.0433814 0.972633 -0.543836 -0.822943 -0.164335 -1.9728 1.73124 -213.082 S_00001
RT 0.807551 -0.566465 0.164254 -0.228262 -0.0433814 0.972633 -0.543836 -0.822943 -0.164335 -1.9728 1.73124 -213.082 S_00001
RT -1 -2.44929e-16 0 2.44929e-16 -1 0 0 0 1 0 0 0 S_00001
ANNOTATED_SEQUENCE: M[MET_p:NtermProteinFull]QFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI[ILE_p:CtermProteinFull]M[MET_p:NtermProteinFull]QFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI[ILE_p:CtermProteinFull]XX S_00001
SYMMETRY_INFO N 2 N_VIRT 2 N_INTERFACE 1 TYPE simple BB_CLONES_SIZE 101 CHI_CLONES_SIZE 101 JUMP_CLONES_SIZE 1 BB_FOLLOWS_SIZE 202 CHI_FOLLOWS_SIZE 202 JUMP_FOLLOWS_SIZE 2 DOFS_SIZE 1 SCORE_MULTIPLY_SIZE 204 BB_CLONES 1,102 2,103 3,104 4,105 5,106 6,107 7,108 8,109 9,110 10,111 11,112 12,113 13,114 14,115 15,116 16,117 17,118 18,119 19,120 20,121 21,122 22,123 23,124 24,125 25,126 26,127 27,128 28,129 29,130 30,131 31,132 32,133 33,134 34,135 35,136 36,137 37,138 38,139 39,140 40,141 41,142 42,143 43,144 44,145 45,146 46,147 47,148 48,149 49,150 50,151 51,152 52,153 53,154 54,155 55,156 56,157 57,158 58,159 59,160 60,161 61,162 62,163 63,164 64,165 65,166 66,167 67,168 68,169 69,170 70,171 71,172 72,173 73,174 74,175 75,176 76,177 77,178 78,179 79,180 80,181 81,182 82,183 83,184 84,185 85,186 86,187 87,188 88,189 89,190 90,191 91,192 92,193 93,194 94,195 95,196 96,197 97,198 98,199 99,200 100,201 101,202 CHI_CLONES 1,102 2,103 3,104 4,105 5,106 6,107 7,108 8,109 9,110 10,111 11,112 12,113 13,114 14,115 15,116 16,117 17,118 18,119 19,120 20,121 21,122 22,123 23,124 24,125 25,126 26,127 27,128 28,129 29,130 30,131 31,132 32,133 33,134 34,135 35,136 36,137 37,138 38,139 39,140 40,141 41,142 42,143 43,144 44,145 45,146 46,147 47,148 48,149 49,150 50,151 51,152 52,153 53,154 54,155 55,156 56,157 57,158 58,159 59,160 60,161 61,162 62,163 63,164 64,165 65,166 66,167 67,168 68,169 69,170 70,171 71,172 72,173 73,174 74,175 75,176 76,177 77,178 78,179 79,180 80,181 81,182 82,183 83,184 84,185 85,186 86,187 87,188 88,189 89,190 90,191 91,192 92,193 93,194 94,195 95,196 96,197 97,198 98,199 99,200 100,201 101,202 JUMP_CLONES 1,2 BB_FOLLOWS 1,0 2,0 3,0 4,0 5,0 6,0 7,0 8,0 9,0 10,0 11,0 12,0 13,0 14,0 15,0 16,0 17,0 18,0 19,0 20,0 21,0 22,0 23,0 24,0 25,0 26,0 27,0 28,0 29,0 30,0 31,0 32,0 33,0 34,0 35,0 36,0 37,0 38,0 39,0 40,0 41,0 42,0 43,0 44,0 45,0 46,0 47,0 48,0 49,0 50,0 51,0 52,0 53,0 54,0 55,0 56,0 57,0 58,0 59,0 60,0 61,0 62,0 63,0 64,0 65,0 66,0 67,0 68,0 69,0 70,0 71,0 72,0 73,0 74,0 75,0 76,0 77,0 78,0 79,0 80,0 81,0 82,0 83,0 84,0 85,0 86,0 87,0 88,0 89,0 90,0 91,0 92,0 93,0 94,0 95,0 96,0 97,0 98,0 99,0 100,0 101,0 102,1 103,2 104,3 105,4 106,5 107,6 108,7 109,8 110,9 111,10 112,11 113,12 114,13 115,14 116,15 117,16 118,17 119,18 120,19 121,20 122,21 123,22 124,23 125,24 126,25 127,26 128,27 129,28 130,29 131,30 132,31 133,32 134,33 135,34 136,35 137,36 138,37 139,38 140,39 141,40 142,41 143,42 144,43 145,44 146,45 147,46 148,47 149,48 150,49 151,50 152,51 153,52 154,53 155,54 156,55 157,56 158,57 159,58 160,59 161,60 162,61 163,62 164,63 165,64 166,65 167,66 168,67 169,68 170,69 171,70 172,71 173,72 174,73 175,74 176,75 177,76 178,77 179,78 180,79 181,80 182,81 183,82 184,83 185,84 186,85 187,86 188,87 189,88 190,89 191,90 192,91 193,92 194,93 195,94 196,95 197,96 198,97 199,98 200,99 201,100 202,101 CHI_FOLLOWS 1,0 2,0 3,0 4,0 5,0 6,0 7,0 8,0 9,0 10,0 11,0 12,0 13,0 14,0 15,0 16,0 17,0 18,0 19,0 20,0 21,0 22,0 23,0 24,0 25,0 26,0 27,0 28,0 29,0 30,0 31,0 32,0 33,0 34,0 35,0 36,0 37,0 38,0 39,0 40,0 41,0 42,0 43,0 44,0 45,0 46,0 47,0 48,0 49,0 50,0 51,0 52,0 53,0 54,0 55,0 56,0 57,0 58,0 59,0 60,0 61,0 62,0 63,0 64,0 65,0 66,0 67,0 68,0 69,0 70,0 71,0 72,0 73,0 74,0 75,0 76,0 77,0 78,0 79,0 80,0 81,0 82,0 83,0 84,0 85,0 86,0 87,0 88,0 89,0 90,0 91,0 92,0 93,0 94,0 95,0 96,0 97,0 98,0 99,0 100,0 101,0 102,1 103,2 104,3 105,4 106,5 107,6 108,7 109,8 110,9 111,10 112,11 113,12 114,13 115,14 116,15 117,16 118,17 119,18 120,19 121,20 122,21 123,22 124,23 125,24 126,25 127,26 128,27 129,28 130,29 131,30 132,31 133,32 134,33 135,34 136,35 137,36 138,37 139,38 140,39 141,40 142,41 143,42 144,43 145,44 146,45 147,46 148,47 149,48 150,49 151,50 152,51 153,52 154,53 155,54 156,55 157,56 158,57 159,58 160,59 161,60 162,61 163,62 164,63 165,64 166,65 167,66 168,67 169,68 170,69 171,70 172,71 173,72 174,73 175,74 176,75 177,76 178,77 179,78 180,79 181,80 182,81 183,82 184,83 185,84 186,85 187,86 188,87 189,88 190,89 191,90 192,91 193,92 194,93 195,94 196,95 197,96 198,97 199,98 200,99 201,100 202,101 JUMP_FOLLOWS 1,0 2,1 DOFS 1,x(50:50;0:0;n2c)angle_x(0:360;0:0;n2c)angle_y(0:360;0:0;n2c)angle_z(0:360;0:0;n2c) SCORE_MULTIPLY 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 S_00001
CHAIN_ENDINGS 101 202 S_00001
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[Anonymous]

As far as I can tell, the snippet you show looks fine. At this point I’m guessing there’s an issue with one of the other structures in the silent file.

The error you’re getting is due specifically to the format of the SYMMETRY_INFO line. “-silent_read_through_errors” should theoretically fix that, but it looks like there may be a problem with the SYMMETRY_INFO reading code interacting with that option.

Try greping out the SYMMETRY_INFO lines. (“grep SYMMETRY_INFO silent.out”). Most of the lines should be more-or-less the same, but you may find that there’s one which has too many or too few entries between CHI_CLONES and JUMP_CLONES. You’ll need to manually delete that structure from your silent file. This would involve deleting the lines from the SCORE line before the bad SYMMETRY_INFO line up to (but not including) the SCORE line after the bad SYMMETRY_INFO line. (Alternatively, you may be able to replace the bad SYMMETRY_INFO line with a good one.)

[Anonymous]

I am using the same version of rosetta. read_through_errors flag you mentioned also gave the same error.
Can you provide any more suggestions…
I am searching but, nowhere I can find solution to similar problem..

[Anonymous]

Are you trying to read in a silent file with symmetric structures? If so, you may want to provide to the the symdef file you used for generating the structures in the first place to the extract_pdbs commandline.

Failing that, could you post an example of what’s in your silent file? The first several hundred lines or so would likely be sufficient.

[Author]

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