diff --git a/rna_tools/tools/triplexibility/data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm.pdb b/rna_tools/tools/triplexibility/data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm.pdb
new file mode 100644
index 000000000..c361d6753
--- /dev/null
+++ b/rna_tools/tools/triplexibility/data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm.pdb
@@ -0,0 +1,67 @@
+ATOM 1 P C A 29 311.625 275.801 304.495 1.00 99.99 P
+ATOM 2 C5' C A 29 310.367 276.034 306.773 1.00 99.99 C
+ATOM 3 O5' C A 29 310.391 275.529 305.448 1.00 99.99 O
+ATOM 4 C4' C A 29 309.047 275.714 307.457 1.00 99.99 C
+ATOM 5 O4' C A 29 308.000 276.564 306.884 1.00 99.99 O
+ATOM 6 C3' C A 29 308.471 274.299 307.326 1.00 99.99 C
+ATOM 7 O3' C A 29 308.992 273.381 308.275 1.00 99.99 O
+ATOM 8 C2' C A 29 306.989 274.536 307.603 1.00 99.99 C
+ATOM 9 O2' C A 29 306.640 274.632 308.963 1.00 99.99 O
+ATOM 10 C1' C A 29 306.761 275.871 306.887 1.00 99.99 C
+ATOM 11 N1 C A 29 306.383 275.575 305.457 1.00 99.99 N
+ATOM 12 C2 C A 29 305.041 275.161 305.238 1.00 99.99 C
+ATOM 13 O2 C A 29 304.271 275.147 306.180 1.00 99.99 O
+ATOM 14 N3 C A 29 304.725 274.804 303.944 1.00 99.99 N
+ATOM 15 C4 C A 29 305.644 274.859 303.003 1.00 99.99 C
+ATOM 16 N4 C A 29 305.262 274.493 301.753 1.00 99.99 N
+ATOM 17 C5 C A 29 307.007 275.277 303.214 1.00 99.99 C
+ATOM 18 C6 C A 29 307.328 275.632 304.488 1.00 99.99 C
+ATOM 19 OP1 C A 29 312.853 275.467 305.211 1.00 99.99 O
+ATOM 20 OP2 C A 29 311.415 275.160 303.164 1.00 99.99 O1-
+ATOM 21 P A A 53 303.170 275.636 296.490 1.00 99.99 P
+ATOM 22 C5' A A 53 300.968 274.243 296.103 1.00 99.99 C
+ATOM 23 O5' A A 53 301.788 275.035 296.991 1.00 99.99 O
+ATOM 24 C4' A A 53 299.967 273.442 296.896 1.00 99.99 C
+ATOM 25 O4' A A 53 300.662 272.506 297.768 1.00 99.99 O
+ATOM 26 C3' A A 53 299.123 274.245 297.863 1.00 99.99 C
+ATOM 27 O3' A A 53 298.064 274.905 297.185 1.00 99.99 O
+ATOM 28 C2' A A 53 298.630 273.173 298.812 1.00 99.99 C
+ATOM 29 O2' A A 53 297.621 272.370 298.225 1.00 99.99 O
+ATOM 30 C1' A A 53 299.895 272.308 298.951 1.00 99.99 C
+ATOM 31 N1 A A 53 299.969 272.801 304.052 1.00 99.99 N
+ATOM 32 C2 A A 53 299.042 272.308 303.201 1.00 99.99 C
+ATOM 33 N3 A A 53 299.090 272.207 301.868 1.00 99.99 N
+ATOM 34 C4 A A 53 300.253 272.681 301.399 1.00 99.99 C
+ATOM 35 C5 A A 53 301.308 273.221 302.142 1.00 99.99 C
+ATOM 36 C6 A A 53 301.117 273.265 303.541 1.00 99.99 C
+ATOM 37 N6 A A 53 302.058 273.762 304.374 1.00 99.99 N
+ATOM 38 N7 A A 53 302.359 273.615 301.340 1.00 99.99 N
+ATOM 39 C8 A A 53 301.939 273.315 300.120 1.00 99.99 C
+ATOM 40 N9 A A 53 300.686 272.755 300.093 1.00 99.99 N
+ATOM 41 OP1 A A 53 302.940 276.309 295.186 1.00 99.99 O
+ATOM 42 OP2 A A 53 303.901 276.365 297.524 1.00 99.99 O1-
+TER
+ATOM 43 P A B 27 307.263 269.083 300.006 1.00 99.99 P
+ATOM 44 C5' A B 27 306.177 269.326 297.631 1.00 99.99 C
+ATOM 45 O5' A B 27 307.268 269.623 298.513 1.00 99.99 O
+ATOM 46 C4' A B 27 306.231 270.232 296.432 1.00 99.99 C
+ATOM 47 O4' A B 27 305.999 271.595 296.882 1.00 99.99 O
+ATOM 48 C3' A B 27 307.573 270.247 295.706 1.00 99.99 C
+ATOM 49 O3' A B 27 307.369 270.476 294.318 1.00 99.99 O
+ATOM 50 C2' A B 27 308.271 271.443 296.349 1.00 99.99 C
+ATOM 51 O2' A B 27 309.297 272.009 295.557 1.00 99.99 O
+ATOM 52 C1' A B 27 307.099 272.408 296.538 1.00 99.99 C
+ATOM 53 N1 A B 27 309.112 276.971 297.786 1.00 99.99 N
+ATOM 54 C2 A B 27 308.986 276.330 296.604 1.00 99.99 C
+ATOM 55 N3 A B 27 308.421 275.146 296.343 1.00 99.99 N
+ATOM 56 C4 A B 27 307.941 274.592 297.465 1.00 99.99 C
+ATOM 57 C5 A B 27 307.991 275.123 298.760 1.00 99.99 C
+ATOM 58 C6 A B 27 308.618 276.382 298.884 1.00 99.99 C
+ATOM 59 N6 A B 27 308.733 277.007 300.078 1.00 99.99 N
+ATOM 60 N7 A B 27 307.401 274.289 299.686 1.00 99.99 N
+ATOM 61 C8 A B 27 306.998 273.260 298.955 1.00 99.99 C
+ATOM 62 N9 A B 27 307.293 273.387 297.620 1.00 99.99 N
+ATOM 63 OP1 A B 27 306.996 267.623 299.970 1.00 99.99 O
+ATOM 64 OP2 A B 27 308.489 269.586 300.672 1.00 99.99 O1-
+TER
+END
diff --git a/rna_tools/tools/triplexibility/data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm_fx.pdb b/rna_tools/tools/triplexibility/data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm_fx.pdb
new file mode 100644
index 000000000..75b3d6ecf
--- /dev/null
+++ b/rna_tools/tools/triplexibility/data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm_fx.pdb
@@ -0,0 +1,67 @@
+ATOM 21 P A A 1 303.170 275.636 296.490 1.00 99.99 P
+ATOM 22 C5' A A 1 300.968 274.243 296.103 1.00 99.99 C
+ATOM 23 O5' A A 1 301.788 275.035 296.991 1.00 99.99 O
+ATOM 24 C4' A A 1 299.967 273.442 296.896 1.00 99.99 C
+ATOM 25 O4' A A 1 300.662 272.506 297.768 1.00 99.99 O
+ATOM 26 C3' A A 1 299.123 274.245 297.863 1.00 99.99 C
+ATOM 27 O3' A A 1 298.064 274.905 297.185 1.00 99.99 O
+ATOM 28 C2' A A 1 298.630 273.173 298.812 1.00 99.99 C
+ATOM 29 O2' A A 1 297.621 272.370 298.225 1.00 99.99 O
+ATOM 30 C1' A A 1 299.895 272.308 298.951 1.00 99.99 C
+ATOM 31 N1 A A 1 299.969 272.801 304.052 1.00 99.99 N
+ATOM 32 C2 A A 1 299.042 272.308 303.201 1.00 99.99 C
+ATOM 33 N3 A A 1 299.090 272.207 301.868 1.00 99.99 N
+ATOM 34 C4 A A 1 300.253 272.681 301.399 1.00 99.99 C
+ATOM 35 C5 A A 1 301.308 273.221 302.142 1.00 99.99 C
+ATOM 36 C6 A A 1 301.117 273.265 303.541 1.00 99.99 C
+ATOM 37 N6 A A 1 302.058 273.762 304.374 1.00 99.99 N
+ATOM 38 N7 A A 1 302.359 273.615 301.340 1.00 99.99 N
+ATOM 39 C8 A A 1 301.939 273.315 300.120 1.00 99.99 C
+ATOM 40 N9 A A 1 300.686 272.755 300.093 1.00 99.99 N
+ATOM 41 OP1 A A 1 302.940 276.309 295.186 1.00 99.99 O
+ATOM 42 OP2 A A 1 303.901 276.365 297.524 1.00 99.99 O1-
+
+ATOM 1 P C A 2 311.625 275.801 304.495 1.00 99.99 P
+ATOM 2 C5' C A 2 310.367 276.034 306.773 1.00 99.99 C
+ATOM 3 O5' C A 2 310.391 275.529 305.448 1.00 99.99 O
+ATOM 4 C4' C A 2 309.047 275.714 307.457 1.00 99.99 C
+ATOM 5 O4' C A 2 308.000 276.564 306.884 1.00 99.99 O
+ATOM 6 C3' C A 2 308.471 274.299 307.326 1.00 99.99 C
+ATOM 7 O3' C A 2 308.992 273.381 308.275 1.00 99.99 O
+ATOM 8 C2' C A 2 306.989 274.536 307.603 1.00 99.99 C
+ATOM 9 O2' C A 2 306.640 274.632 308.963 1.00 99.99 O
+ATOM 10 C1' C A 2 306.761 275.871 306.887 1.00 99.99 C
+ATOM 11 N1 C A 2 306.383 275.575 305.457 1.00 99.99 N
+ATOM 12 C2 C A 2 305.041 275.161 305.238 1.00 99.99 C
+ATOM 13 O2 C A 2 304.271 275.147 306.180 1.00 99.99 O
+ATOM 14 N3 C A 2 304.725 274.804 303.944 1.00 99.99 N
+ATOM 15 C4 C A 2 305.644 274.859 303.003 1.00 99.99 C
+ATOM 16 N4 C A 2 305.262 274.493 301.753 1.00 99.99 N
+ATOM 17 C5 C A 2 307.007 275.277 303.214 1.00 99.99 C
+ATOM 18 C6 C A 2 307.328 275.632 304.488 1.00 99.99 C
+ATOM 19 OP1 C A 2 312.853 275.467 305.211 1.00 99.99 O
+ATOM 20 OP2 C A 2 311.415 275.160 303.164 1.00 99.99 O1-
+
+ATOM 43 P A A 3 307.263 269.083 300.006 1.00 99.99 P
+ATOM 44 C5' A A 3 306.177 269.326 297.631 1.00 99.99 C
+ATOM 45 O5' A A 3 307.268 269.623 298.513 1.00 99.99 O
+ATOM 46 C4' A A 3 306.231 270.232 296.432 1.00 99.99 C
+ATOM 47 O4' A A 3 305.999 271.595 296.882 1.00 99.99 O
+ATOM 48 C3' A A 3 307.573 270.247 295.706 1.00 99.99 C
+ATOM 49 O3' A A 3 307.369 270.476 294.318 1.00 99.99 O
+ATOM 50 C2' A A 3 308.271 271.443 296.349 1.00 99.99 C
+ATOM 51 O2' A A 3 309.297 272.009 295.557 1.00 99.99 O
+ATOM 52 C1' A A 3 307.099 272.408 296.538 1.00 99.99 C
+ATOM 53 N1 A A 3 309.112 276.971 297.786 1.00 99.99 N
+ATOM 54 C2 A A 3 308.986 276.330 296.604 1.00 99.99 C
+ATOM 55 N3 A A 3 308.421 275.146 296.343 1.00 99.99 N
+ATOM 56 C4 A A 3 307.941 274.592 297.465 1.00 99.99 C
+ATOM 57 C5 A A 3 307.991 275.123 298.760 1.00 99.99 C
+ATOM 58 C6 A A 3 308.618 276.382 298.884 1.00 99.99 C
+ATOM 59 N6 A A 3 308.733 277.007 300.078 1.00 99.99 N
+ATOM 60 N7 A A 3 307.401 274.289 299.686 1.00 99.99 N
+ATOM 61 C8 A A 3 306.998 273.260 298.955 1.00 99.99 C
+ATOM 62 N9 A A 3 307.293 273.387 297.620 1.00 99.99 N
+ATOM 63 OP1 A A 3 306.996 267.623 299.970 1.00 99.99 O
+ATOM 64 OP2 A A 3 308.489 269.586 300.672 1.00 99.99 O1-
+
diff --git a/rna_tools/tools/triplexibility/data/still-wrong/312.pdb b/rna_tools/tools/triplexibility/data/still-wrong/312.pdb
new file mode 100644
index 000000000..f8c327198
--- /dev/null
+++ b/rna_tools/tools/triplexibility/data/still-wrong/312.pdb
@@ -0,0 +1,68 @@
+ATOM 43 P A A 3 307.263 269.083 300.006 1.00 99.99 P
+ATOM 44 C5' A A 3 306.177 269.326 297.631 1.00 99.99 C
+ATOM 45 O5' A A 3 307.268 269.623 298.513 1.00 99.99 O
+ATOM 46 C4' A A 3 306.231 270.232 296.432 1.00 99.99 C
+ATOM 47 O4' A A 3 305.999 271.595 296.882 1.00 99.99 O
+ATOM 48 C3' A A 3 307.573 270.247 295.706 1.00 99.99 C
+ATOM 49 O3' A A 3 307.369 270.476 294.318 1.00 99.99 O
+ATOM 50 C2' A A 3 308.271 271.443 296.349 1.00 99.99 C
+ATOM 51 O2' A A 3 309.297 272.009 295.557 1.00 99.99 O
+ATOM 52 C1' A A 3 307.099 272.408 296.538 1.00 99.99 C
+ATOM 53 N1 A A 3 309.112 276.971 297.786 1.00 99.99 N
+ATOM 54 C2 A A 3 308.986 276.330 296.604 1.00 99.99 C
+ATOM 55 N3 A A 3 308.421 275.146 296.343 1.00 99.99 N
+ATOM 56 C4 A A 3 307.941 274.592 297.465 1.00 99.99 C
+ATOM 57 C5 A A 3 307.991 275.123 298.760 1.00 99.99 C
+ATOM 58 C6 A A 3 308.618 276.382 298.884 1.00 99.99 C
+ATOM 59 N6 A A 3 308.733 277.007 300.078 1.00 99.99 N
+ATOM 60 N7 A A 3 307.401 274.289 299.686 1.00 99.99 N
+ATOM 61 C8 A A 3 306.998 273.260 298.955 1.00 99.99 C
+ATOM 62 N9 A A 3 307.293 273.387 297.620 1.00 99.99 N
+ATOM 63 OP1 A A 3 306.996 267.623 299.970 1.00 99.99 O
+ATOM 64 OP2 A A 3 308.489 269.586 300.672 1.00 99.99 O1-
+
+ATOM 21 P A A 1 303.170 275.636 296.490 1.00 99.99 P
+ATOM 22 C5' A A 1 300.968 274.243 296.103 1.00 99.99 C
+ATOM 23 O5' A A 1 301.788 275.035 296.991 1.00 99.99 O
+ATOM 24 C4' A A 1 299.967 273.442 296.896 1.00 99.99 C
+ATOM 25 O4' A A 1 300.662 272.506 297.768 1.00 99.99 O
+ATOM 26 C3' A A 1 299.123 274.245 297.863 1.00 99.99 C
+ATOM 27 O3' A A 1 298.064 274.905 297.185 1.00 99.99 O
+ATOM 28 C2' A A 1 298.630 273.173 298.812 1.00 99.99 C
+ATOM 29 O2' A A 1 297.621 272.370 298.225 1.00 99.99 O
+ATOM 30 C1' A A 1 299.895 272.308 298.951 1.00 99.99 C
+ATOM 31 N1 A A 1 299.969 272.801 304.052 1.00 99.99 N
+ATOM 32 C2 A A 1 299.042 272.308 303.201 1.00 99.99 C
+ATOM 33 N3 A A 1 299.090 272.207 301.868 1.00 99.99 N
+ATOM 34 C4 A A 1 300.253 272.681 301.399 1.00 99.99 C
+ATOM 35 C5 A A 1 301.308 273.221 302.142 1.00 99.99 C
+ATOM 36 C6 A A 1 301.117 273.265 303.541 1.00 99.99 C
+ATOM 37 N6 A A 1 302.058 273.762 304.374 1.00 99.99 N
+ATOM 38 N7 A A 1 302.359 273.615 301.340 1.00 99.99 N
+ATOM 39 C8 A A 1 301.939 273.315 300.120 1.00 99.99 C
+ATOM 40 N9 A A 1 300.686 272.755 300.093 1.00 99.99 N
+ATOM 41 OP1 A A 1 302.940 276.309 295.186 1.00 99.99 O
+ATOM 42 OP2 A A 1 303.901 276.365 297.524 1.00 99.99 O1-
+
+ATOM 1 P C A 2 311.625 275.801 304.495 1.00 99.99 P
+ATOM 2 C5' C A 2 310.367 276.034 306.773 1.00 99.99 C
+ATOM 3 O5' C A 2 310.391 275.529 305.448 1.00 99.99 O
+ATOM 4 C4' C A 2 309.047 275.714 307.457 1.00 99.99 C
+ATOM 5 O4' C A 2 308.000 276.564 306.884 1.00 99.99 O
+ATOM 6 C3' C A 2 308.471 274.299 307.326 1.00 99.99 C
+ATOM 7 O3' C A 2 308.992 273.381 308.275 1.00 99.99 O
+ATOM 8 C2' C A 2 306.989 274.536 307.603 1.00 99.99 C
+ATOM 9 O2' C A 2 306.640 274.632 308.963 1.00 99.99 O
+ATOM 10 C1' C A 2 306.761 275.871 306.887 1.00 99.99 C
+ATOM 11 N1 C A 2 306.383 275.575 305.457 1.00 99.99 N
+ATOM 12 C2 C A 2 305.041 275.161 305.238 1.00 99.99 C
+ATOM 13 O2 C A 2 304.271 275.147 306.180 1.00 99.99 O
+ATOM 14 N3 C A 2 304.725 274.804 303.944 1.00 99.99 N
+ATOM 15 C4 C A 2 305.644 274.859 303.003 1.00 99.99 C
+ATOM 16 N4 C A 2 305.262 274.493 301.753 1.00 99.99 N
+ATOM 17 C5 C A 2 307.007 275.277 303.214 1.00 99.99 C
+ATOM 18 C6 C A 2 307.328 275.632 304.488 1.00 99.99 C
+ATOM 19 OP1 C A 2 312.853 275.467 305.211 1.00 99.99 O
+ATOM 20 OP2 C A 2 311.415 275.160 303.164 1.00 99.99 O1-
+
+
diff --git a/rna_tools/tools/triplexibility/data/still-wrong/t2-4.pdb b/rna_tools/tools/triplexibility/data/still-wrong/t2-4.pdb
new file mode 100644
index 000000000..4da4bd9ad
--- /dev/null
+++ b/rna_tools/tools/triplexibility/data/still-wrong/t2-4.pdb
@@ -0,0 +1,67 @@
+ATOM 1 P A A 53 309.118 281.472 306.787 1.00216.12 P
+ATOM 2 C5' A A 53 307.172 279.945 307.674 1.00253.23 C
+ATOM 3 O5' A A 53 308.153 280.194 306.681 1.00235.46 O
+ATOM 4 C4' A A 53 307.274 278.551 308.309 1.00271.26 C
+ATOM 5 O4' A A 53 306.387 277.573 307.803 1.00274.76 O
+ATOM 6 C3' A A 53 308.661 277.964 308.186 1.00279.17 C
+ATOM 7 O3' A A 53 309.573 278.620 309.042 1.00282.50 O
+ATOM 8 C2' A A 53 308.417 276.467 308.423 1.00277.57 C
+ATOM 9 O2' A A 53 308.241 275.992 309.751 1.00273.04 O
+ATOM 10 C1' A A 53 307.081 276.335 307.731 1.00278.25 C
+ATOM 11 N1 A A 53 304.351 275.123 303.744 1.00294.92 N
+ATOM 12 C2 A A 53 304.031 275.302 305.016 1.00295.61 C
+ATOM 13 N3 A A 53 304.859 275.477 306.051 1.00292.57 N
+ATOM 14 C4 A A 53 306.149 275.546 305.572 1.00288.50 C
+ATOM 15 C5 A A 53 306.626 275.373 304.310 1.00289.97 C
+ATOM 16 C6 A A 53 305.606 275.195 303.400 1.00294.13 C
+ATOM 17 N6 A A 53 305.775 275.118 302.135 1.00297.45 N
+ATOM 18 N7 A A 53 308.013 275.479 304.256 1.00286.88 N
+ATOM 19 C8 A A 53 308.314 275.892 305.462 1.00284.70 C
+ATOM 20 N9 A A 53 307.227 275.943 306.315 1.00283.56 N
+ATOM 21 OP1 A A 53 309.549 281.701 308.183 1.00216.18 O
+ATOM 22 OP2 A A 53 310.069 281.525 305.669 1.00211.30 O1-
+TER
+ATOM 23 P A B 27 295.653 270.783 300.135 1.00119.29 P
+ATOM 24 C5' A B 27 297.608 269.806 298.646 1.00124.09 C
+ATOM 25 O5' A B 27 296.498 270.692 298.778 1.00116.84 O
+ATOM 26 C4' A B 27 298.604 270.387 297.645 1.00125.53 C
+ATOM 27 O4' A B 27 298.623 271.795 297.821 1.00112.51 O
+ATOM 28 C3' A B 27 300.051 269.848 297.754 1.00131.59 C
+ATOM 29 O3' A B 27 300.320 268.757 296.859 1.00136.80 O
+ATOM 30 C2' A B 27 300.821 271.136 297.406 1.00123.34 C
+ATOM 31 O2' A B 27 300.873 271.377 296.000 1.00126.16 O
+ATOM 32 C1' A B 27 299.944 272.209 298.072 1.00120.15 C
+ATOM 33 N1 A B 27 303.441 273.472 301.457 1.00 0.00 N
+ATOM 34 C2 A B 27 303.405 273.547 300.145 1.00 0.00 C
+ATOM 35 N3 A B 27 302.457 273.101 299.343 1.00 0.00 N
+ATOM 36 C4 A B 27 301.384 272.671 300.054 1.00 0.00 C
+ATOM 37 C5 A B 27 301.255 272.568 301.406 1.00 0.00 C
+ATOM 38 C6 A B 27 302.390 272.991 302.104 1.00 0.00 C
+ATOM 39 N6 A B 27 302.510 272.979 303.407 1.00 0.00 N
+ATOM 40 N7 A B 27 300.005 272.071 301.769 1.00 0.00 N
+ATOM 41 C8 A B 27 299.403 271.983 300.614 1.00 0.00 C
+ATOM 42 N9 A B 27 300.207 272.250 299.527 1.00 0.00 N
+ATOM 43 OP1 A B 27 294.537 269.823 299.943 1.00124.15 O
+ATOM 44 OP2 A B 27 296.588 270.536 301.244 1.00104.17 O1-
+ATOM 45 P C B 29 308.228 267.714 297.766 1.00240.85 P
+ATOM 46 C5' C B 29 307.188 269.097 295.731 1.00274.02 C
+ATOM 47 O5' C B 29 308.158 268.976 296.768 1.00259.17 O
+ATOM 48 C4' C B 29 306.900 270.552 295.294 1.00292.45 C
+ATOM 49 O4' C B 29 306.126 271.274 296.242 1.00291.83 O
+ATOM 50 C3' C B 29 308.134 271.422 295.059 1.00305.45 C
+ATOM 51 O3' C B 29 308.895 271.147 293.881 1.00326.43 O
+ATOM 52 C2' C B 29 307.480 272.813 295.062 1.00301.06 C
+ATOM 53 O2' C B 29 306.706 273.077 293.882 1.00303.89 O
+ATOM 54 C1' C B 29 306.543 272.647 296.267 1.00290.90 C
+ATOM 55 N1 C B 29 307.115 272.919 297.634 1.00 0.00 N
+ATOM 56 C2 C B 29 308.457 273.299 297.903 1.00 0.00 C
+ATOM 57 O2 C B 29 309.357 273.217 297.070 1.00 0.00 O
+ATOM 58 N3 C B 29 308.847 273.566 299.172 1.00 0.00 N
+ATOM 59 C4 C B 29 307.979 273.510 300.144 1.00 0.00 C
+ATOM 60 N4 C B 29 308.428 273.836 301.319 1.00 0.00 N
+ATOM 61 C5 C B 29 306.676 272.986 299.971 1.00 0.00 C
+ATOM 62 C6 C B 29 306.267 272.737 298.701 1.00 0.00 C
+ATOM 63 OP1 C B 29 307.478 266.587 297.160 1.00241.04 O
+ATOM 64 OP2 C B 29 309.635 267.450 298.137 1.00246.10 O1-
+TER
+END
diff --git a/rna_tools/tools/triplexibility/test.sh b/rna_tools/tools/triplexibility/test.sh
new file mode 100755
index 000000000..f3a79c8c1
--- /dev/null
+++ b/rna_tools/tools/triplexibility/test.sh
@@ -0,0 +1,19 @@
+set -x
+#python splix.py # --d2 UA --growth 1 # wt U57:A27.A53
+#python seqs.py AAG-0 # U57:A27.A53
+#python seqs.py AUG-1 # suppresion
+#python seqs.py ACG-0.5 # half-suppression
+#python seqs.py AGG-0 #
+#open splix.csv
+
+# triplexibility.py
+#./triplexibility.py -t data/still-wrong/t2-4.pdb data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm.pdb
+#./triplexibility.py --triple-mode --tseq UUU --way backbone+sugar -t data/still-wrong/t2-4.pdb data/still-wrong/* --save --debug
+
+./triplexibility.py --triple-mode --tseq aca --way backbone+sugar -t data/still-wrong/t2-4.pdb data/still-wrong/0.90-Triple_tHW_tHH_ACA_rpr_renm_fx.pdb --save --debug
+# still-wrong/*
+
+#--verbose
+#0.90-Triple_tHW_tHH_ACA_rpr_renm.pdb --save --triple-mode
+#./triplexibility.py --triple-mode --way c1+Nx -t data/still-wrong/t2-4.pdb data/still-wrong/*
+#0.90-Triple_tHW_tHH_ACA_rpr_renm.pdb
diff --git a/rna_tools/tools/triplexibility/triplexibility.py b/rna_tools/tools/triplexibility/triplexibility.py
index 20f6d7a27..1dea8ed90 100755
--- a/rna_tools/tools/triplexibility/triplexibility.py
+++ b/rna_tools/tools/triplexibility/triplexibility.py
@@ -159,7 +159,9 @@ def chunks(lst, n):
sup_min = None
seq_min = 'not yet obtained, rmsd rejected!'
p_min = None
+
rms = -1
+
for p in per:
patoms = []
for i in p: # p=(1, 2, 3)
@@ -248,6 +250,7 @@ def chunks(lst, n):
set_chain_for_struc(fout, 'A', save_file_inplace=True)
# and now run this to sort into 1 2 3
+
r = RNAStructure(fout)
remarks = r.get_remarks_text()
r1 = r.get_res_text('A', 1)
diff --git a/rna_tools/tools/webserver-engine/app/templates/diffpdb.html b/rna_tools/tools/webserver-engine/app/templates/diffpdb.html
index 57034fff1..84a465fd8 100644
--- a/rna_tools/tools/webserver-engine/app/templates/diffpdb.html
+++ b/rna_tools/tools/webserver-engine/app/templates/diffpdb.html
@@ -51,6 +51,7 @@
function go() {
$.ajax({
url: "/run/diffpdb/{{ j.job_id }}",
+ data: { names: $('#names').is(':checked')},
success: function(d) {
$("#log_txt").html(d['log']);
if (d['reload']==true){
@@ -81,6 +82,10 @@
diffpdb
+
+
{{ log | safe }}
The raw output files for each step of the pipeline can be found here