Interface_ #8
Comments
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fixed by 1cecca9 |
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Traceback (most recent call last): |
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Hi please create another issue with the full terminal output and the trace. I suspect this is just too many contacts trying to be plot. try switching the time traces off |
I can get the result including graphical output but still there is an error at the end
(base) lepoard@lepoard-GP63-Leopard-8RE:/media/lepoard/storage1/Data/actor-f$ interface_ctc_analyzer.py prot1.pdb run1.xtc run2.xtc run3.xtc run4.xtc --frag_idxs_group_1 0,1 --frag_idxs_group_2 2,3 --short_AAs --t_unit mus --sort_by_av_ctcs --curve_color Hobat --graphic_dpi 300 --graphic_ext png --n_smooth_hw 20 --BW_uniprot adrb2_human --CGN 3SN6 --ctc_cutoff_Ang 4 --interface_cutoff_Ang 25 --n_ctcs 40
Will compute contact frequencies for the files:
run1.xtc
run2.xtc
run3.xtc
run4.xtc
with a stride of 1 frames.
Auto-detected fragments with method resSeq
fragment 0 with 203 AAs GLU30( 0)-LYS232 (202 ) (0)
fragment 1 with 78 AAs PHE264( 203)-CYSP341(280 ) (1)
fragment 2 with 69 AAs CYSP2( 281)-GLY70 (349 ) (2)
fragment 3 with 310 AAs ASP85( 350)-LEU394 (659 ) (3)
fragment 4 with 339 AAs SER2( 660)-ASN340 (998 ) (4)
fragment 5 with 67 AAs ALA2( 999)-CYSG68 (1065) (5)
fragment 6 with 3 AAs P0G395(1066)-MG397 (1068) (6)
requesting https://gpcrdb.org/services/residues/extended/adrb2_human ...
done!
BW-numbering aligns best with fragments: [0, 1] (first-last: GLU30-CYSP341).
Input alternative in a format 1,2-6,10,20-25 or hit enter
5
166 ASN196 5.35 5.35 1
167 GLN197 5.36 5.36 1
168 ALA198 5.37 5.37 1
169 TYR199 5.38 5.38 1
170 ALA200 5.39 5.39 1
171 ILE201 5.40 5.40 1
172 ALA202 5.41 5.41 1
173 SER203 5.42 5.42 1
174 SER204 5.43 5.43 1
175 ILE205 5.44 5.44 1
176 VAL206 5.45 5.45 1
177 SER207 5.46 5.46 1
178 PHE208 5.47 5.47 1
179 TYR209 5.48 5.48 1
180 VAL210 5.49 5.49 1
181 PRO211 5.50 5.50 1
182 LEU212 5.51 5.51 1
183 VAL213 5.52 5.52 1
184 ILE214 5.53 5.53 1
185 MET215 5.54 5.54 1
186 VAL216 5.55 5.55 1
187 PHE217 5.56 5.56 1
188 VAL218 5.57 5.57 1
189 TYR219 5.58 5.58 1
190 SER220 5.59 5.59 1
191 ARG221 5.60 5.60 1
192 VAL222 5.61 5.61 1
193 PHE223 5.62 5.62 1
194 GLN224 5.63 5.63 1
195 GLU225 5.64 5.64 1
196 CYS226 None 5.65 1
197 LYS227 5.66 5.66 1
198 ARG228 5.67 5.67 1
199 GLN229 5.68 5.68 1
200 LEU230 5.69 5.69 1
201 GLN231 5.70 5.70 1
The consensus was kept, I am relabelling these:
5.65
INFO: these are the BW fragments mapped onto your topology
TM6 with 37 AAs LYS232( 202)-GLN299 (238 ) (TM6) 6.25-6.61
more than 1 fragments present. Input the ones to keep [0 1]0
TM1 with 32 AAs GLU30( 0)-PHE61 (31 ) (TM1)
ICL1 with 4 AAs GLU62( 32)-GLN65 (35 ) (ICL1)
TM2 with 31 AAs THR66( 36)-MET96 (66 ) (TM2)
ECL1 with 4 AAs MET98( 68)-PHE101 (71 ) (ECL1)
TM3 with 36 AAs GLY102( 72)-SER137 (107 ) (TM3)
ICL2 with 8 AAs PRO138( 108)-LEU145 (115 ) (ICL2)
TM4 with 27 AAs THR146( 116)-HIS172 (142 ) (TM4)
ECL2 with 3 AAs CYS191( 161)-PHE193 (163 ) (ECL2)
TM5 with 36 AAs ASN196( 166)-GLN231 (201 ) (TM5)
TM6 with 1 AAs LYS232( 202)-LYS232 (202 ) (TM6)
TM7 with 25 AAs ARG304( 243)-ARG328 (267 ) (TM7)
H8 with 11 AAs SER329( 268)-LEU339 (278 ) (H8)
Hit enter to continue!
CGN-numbering aligns best with fragments: [2, 3] (first-last: CYSP2-LEU394).
Input alternative in a format 1,2-6,10,20-25 or hit enter
H.hehf
452 GLN187 H.hehf.1 H.hehf.1 1
453 ALA188 None H.hehf.2 1
454 ASP189 H.hehf.3 H.hehf.3 1
455 TYR190 H.hehf.4 H.hehf.4 1
456 VAL191 H.hehf.5 H.hehf.5 1
457 PRO192 H.hehf.6 H.hehf.6 1
458 SER193 H.hehf.7 H.hehf.7 1
The consensus was kept, I am relabelling these:
H.hehf.2
G.hfs2
465 CYS200 G.hfs2.1 G.hfs2.1 1
466 ARG201 G.hfs2.2 G.hfs2.2 1
467 VAL202 G.hfs2.3 G.hfs2.3 1
468 LEU203 None G.hfs2.4 1
469 THR204 None G.hfs2.5 1
470 SER205 G.hfs2.6 G.hfs2.6 1
471 GLY206 G.hfs2.7 G.hfs2.7 1
The consensus was kept, I am relabelling these:
G.hfs2.4
G.hfs2.5
G.s4h3
515 SER250 G.s4h3.1 G.s4h3.1 1
516 SER251 G.s4h3.2 G.s4h3.2 1
517 SER252 G.s4h3.3 G.s4h3.3 1
518 TYR253 G.s4h3.4 G.s4h3.4 1
519 ASN254 None G.s4h3.5 1
520 VAL255 None G.s4h3.6 1
521 LEU256 None G.s4h3.7 1
522 ILE257 None G.s4h3.8 1
523 ARG258 None G.s4h3.9 1
524 GLU259 None G.s4h3.10 1
525 ASP260 None G.s4h3.11 1
526 ASN261 G.s4h3.5 G.s4h3.12 0
527 GLN262 None G.s4h3.13 0
528 THR263 G.s4h3.14 G.s4h3.14 0
529 ASN264 G.s4h3.15 G.s4h3.15 0
Consensus wasn't kept. Nothing done!
INFO: these are the CGN fragments mapped onto your topology
G.HN with 28 AAs THR9( 288)-VAL36 (315 ) (G.HN)
G.hns1 with 3 AAs TYR37( 316)-ALA39 (318 ) (G.hns1)
G.S1 with 7 AAs THR40( 319)-LEU46 (325 ) (G.S1)
G.s1h1 with 6 AAs GLY47( 326)-GLY52 (331 ) (G.s1h1)
G.H1 with 7 AAs LYS53( 332)-GLN59 (338 ) (G.H1)
H.HA with 26 AAs LYS88( 353)-LEU113 (378 ) (H.HA)
H.hahb with 9 AAs VAL114( 379)-PRO122 (387 ) (H.hahb)
H.HB with 14 AAs GLU123( 388)-ASN136 (401 ) (H.HB)
H.hbhc with 7 AAs VAL137( 402)-PRO143 (408 ) (H.hbhc)
H.HC with 12 AAs PRO144( 409)-GLU155 (420 ) (H.HC)
H.hchd with 1 AAs ASP156( 421)-ASP156 (421 ) (H.hchd)
H.HD with 12 AAs GLU157( 422)-GLU168 (433 ) (H.HD)
H.hdhe with 5 AAs TYR169( 434)-ASP173 (438 ) (H.hdhe)
H.HE with 13 AAs CYS174( 439)-LYS186 (451 ) (H.HE)
H.hehf with 7 AAs GLN187( 452)-SER193 (458 ) (H.hehf)
H.HF with 6 AAs ASP194( 459)-ARG199 (464 ) (H.HF)
G.hfs2 with 5 AAs CYS200( 465)-GLY206 (471 ) (G.hfs2)
G.S2 with 8 AAs ILE207( 472)-VAL214 (479 ) (G.S2)
G.s2s3 with 2 AAs ASP215( 480)-LYS216 (481 ) (G.s2s3)
G.S3 with 8 AAs VAL217( 482)-VAL224 (489 ) (G.S3)
G.s3h2 with 3 AAs GLY225( 490)-GLN227 (492 ) (G.s3h2)
G.H2 with 10 AAs ARG228( 493)-CYS237 (502 ) (G.H2)
G.h2s4 with 5 AAs PHE238( 503)-THR242 (507 ) (G.h2s4)
G.S4 with 7 AAs ALA243( 508)-ALA249 (514 ) (G.S4)
G.s4h3 with 7 AAs SER250( 515)-ASN264 (529 ) (G.s4h3)
G.H3 with 18 AAs ARG265( 530)-LEU282 (547 ) (G.H3)
G.h3s5 with 3 AAs ARG283( 548)-ILE285 (550 ) (G.h3s5)
G.S5 with 7 AAs SER286( 551)-ASN292 (557 ) (G.S5)
G.s5hg with 1 AAs LYS293( 558)-LYS293 (558 ) (G.s5hg)
G.HG with 17 AAs GLN294( 559)-ASP310 (575 ) (G.HG)
G.hgh4 with 10 AAs TYR311( 576)-THR320 (585 ) (G.hgh4)
G.H4 with 27 AAs PRO321( 586)-ARG347 (612 ) (G.H4)
G.h4s6 with 11 AAs ILE348( 613)-TYR358 (623 ) (G.h4s6)
G.S6 with 5 AAs CYS359( 624)-PHE363 (628 ) (G.S6)
G.s6h5 with 5 AAs THR364( 629)-ASP368 (633 ) (G.s6h5)
G.H5 with 26 AAs THR369( 634)-LEU394 (659 ) (G.H5)
Hit enter to continue!
Computing distances in the interface between fragments
0, 1
and
2, 3.
The interface is defined by the residues within 25.0 Angstrom of each other in the reference topology.
Computing interface...done!
From 106499 potential group_1-group_2 distances, the interface was reduced to only 2389 potential contacts.
If this number is still too high (i.e. the computation is too slow) consider using a smaller interface cutoff
0%| | 0/4 [00:00<?, ?it/s] 25%|████████████████████████████████████████████ | 1/4 [00:28<01:24, 28.18s/it] 50%|████████████████████████████████████████████████████████████████████████████████████████ | 2/4 [00:54<00:55, 27.71s/it] 75%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 3/4 [01:21<00:27, 27.50s/it]100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [01:50<00:00, 27.62s/it]
0 0.73 101 657 R131@3.50 - E392@G.H5.24 0.73
1 0.56 108 650 P138@34.50 - R385@G.H5.17 1.28
2 0.51 209 659 K270@6.32 - L394@G.H5.26 1.79
3 0.47 268 656 S329@8.47 - Y391@G.H5.23 2.27
4 0.47 273 317 I334@8.52 - R38@G.hns1.2 2.74
5 0.43 112 650 Q142@34.54 - R385@G.H5.17 3.17
6 0.38 33 317 R63@12.49 - R38@G.hns1.2 3.55
7 0.37 206 659 K267@6.29 - L394@G.H5.26 3.92
8 0.35 277 313 E338@8.56 - K34@G.HN.51 4.27
9 0.34 206 658 K267@6.29 - L393@G.H5.25 4.61
10 0.34 39 656 N69@2.40 - Y391@G.H5.23 4.95
11 0.34 270 656 D331@8.49 - Y391@G.H5.23 5.29
12 0.33 33 652 R63@12.49 - H387@G.H5.19 5.63
13 0.33 209 658 K270@6.32 - L393@G.H5.25 5.96
14 0.33 109 647 F139@34.51 - I382@G.H5.14 6.29
15 0.33 268 655 S329@8.47 - Q390@G.H5.22 6.61
16 0.31 213 658 T274@6.36 - L393@G.H5.25 6.92
17 0.30 109 650 F139@34.51 - R385@G.H5.17 7.23
18 0.30 111 650 Y141@34.53 - R385@G.H5.17 7.53
19 0.30 33 656 R63@12.49 - Y391@G.H5.23 7.83
20 0.29 205 658 L266@6.28 - L393@G.H5.25 8.12
21 0.28 273 314 I334@8.52 - Q35@G.HN.52 8.40
22 0.27 112 653 Q142@34.54 - L388@G.H5.20 8.67
23 0.27 269 317 P330@8.48 - R38@G.hns1.2 8.94
24 0.27 109 625 F139@34.51 - Y360@G.S6.2 9.20
25 0.27 36 653 T66@2.37 - L388@G.H5.20 9.47
26 0.26 32 481 E62@12.48 - K216@G.s2s3.2 9.72
27 0.26 199 621 Q229@5.68 - R356@G.h4s6.12 9.98
28 0.25 109 643 F139@34.51 - D378@G.H5.10 10.24
29 0.25 112 646 Q142@34.54 - D381@G.H5.13 10.49
30 0.25 108 625 P138@34.50 - Y360@G.S6.2 10.74
31 0.25 38 656 T68@2.39 - Y391@G.H5.23 10.99
32 0.24 210 658 A271@6.33 - L393@G.H5.25 11.23
33 0.24 109 646 F139@34.51 - D381@G.H5.13 11.48
34 0.24 203 620 F264@6.26 - G355@G.h4s6.11 11.72
35 0.24 105 654 I135@3.54 - R389@G.H5.21 11.96
36 0.23 203 621 F264@6.26 - R356@G.h4s6.12 12.19
37 0.23 195 621 E225@5.64 - R356@G.h4s6.12 12.42
38 0.22 273 310 I334@8.52 - Q31@G.HN.48 12.65
39 0.22 216 659 I277@6.39 - L394@G.H5.26 12.87
0 PHE139@34.51 1.39
1 ARG63@12.49 1.01
2 ILE334@8.52 0.98
3 GLN142@34.54 0.95
4 LYS270@6.32 0.85
5 PRO138@34.50 0.81
6 SER329@8.47 0.80
7 ARG131@3.50 0.73
8 LYS267@6.29 0.71
9 PHE264@6.26 0.48
10 GLU338@8.56 0.35
11 ASN69@2.40 0.34
12 ASP331@8.49 0.34
13 THR274@6.36 0.31
14 TYR141@34.53 0.30
15 LEU266@6.28 0.29
16 PRO330@8.48 0.27
17 THR66@2.37 0.27
18 GLU62@12.48 0.26
19 GLN229@5.68 0.26
20 THR68@2.39 0.25
21 ALA271@6.33 0.24
22 ILE135@3.54 0.24
23 GLU225@5.64 0.23
24 ILE277@6.39 0.22
0 TYR391@G.H5.23 1.70
1 ARG385@G.H5.17 1.60
2 LEU393@G.H5.25 1.52
3 ARG38@G.hns1.2 1.12
4 LEU394@G.H5.26 1.10
5 GLU392@G.H5.24 0.73
6 ARG356@G.h4s6.12 0.72
7 LEU388@G.H5.20 0.53
8 TYR360@G.S6.2 0.52
9 ASP381@G.H5.13 0.49
10 LYS34@G.HN.51 0.35
11 HIS387@G.H5.19 0.33
12 ILE382@G.H5.14 0.33
13 GLN390@G.H5.22 0.33
14 GLN35@G.HN.52 0.28
15 LYS216@G.s2s3.2 0.26
16 ASP378@G.H5.10 0.25
17 GLY355@G.h4s6.11 0.24
18 ARG389@G.H5.21 0.24
19 GLN31@G.HN.48 0.22
The following files have been created
./interface.overall.png
./interface.overall.xlsx
Traceback (most recent call last):
File "/home/lepoard/anaconda3/bin/interface_ctc_analyzer.py", line 4, in
import('pkg_resources').run_script('mdciao==0.1', 'interface_ctc_analyzer.py')
File "/home/lepoard/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/lepoard/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1469, in run_script
exec(script_code, namespace, namespace)
File "/home/lepoard/anaconda3/lib/python3.7/site-packages/mdciao-0.1-py3.7.egg/EGG-INFO/scripts/interface_ctc_analyzer.py", line 13, in
File "/home/lepoard/anaconda3/lib/python3.7/site-packages/mdciao-0.1-py3.7.egg/mdciao/command_line_tools.py", line 1039, in interface
File "/home/lepoard/anaconda3/lib/python3.7/site-packages/mdciao-0.1-py3.7.egg/mdciao/contacts.py", line 1107, in plot_timedep_ctcs
UnboundLocalError: local variable 'axes_iter' referenced before assignment
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