Comments (5)
wojdyr
commented on June 1, 2024
In usual PDB files the TER record ends polymer but not "chain".
Each chain has a different name - that's how they are separated.
I don't know what can be done here.
How would this file look like if there were ligands (non-polymers) in chains?
from gemmi.
sizmailov
commented on June 1, 2024
The version for MD has ions and water. I guess it's sufficient example.
grep -B 4 -A 2 -m 40 TER trouble.pdb
ATOM 2077 HG23 VAL 138 -3.898 2.156 41.081 1.00 0.00
ATOM 2078 C VAL 138 -3.121 4.086 42.599 1.00 0.00
ATOM 2079 O VAL 138 -3.398 3.429 43.629 1.00 0.00
ATOM 2080 OXT VAL 138 -3.861 4.969 42.117 1.00 0.00
TER
ATOM 2081 N VAL 139 -23.085 -10.959 -28.434 1.00 0.00
ATOM 2082 H1 VAL 139 -22.568 -11.857 -28.339 1.00 0.00
--
ATOM 4157 HG23 VAL 276 -35.856 2.156 -41.081 1.00 0.00
ATOM 4158 C VAL 276 -36.633 4.086 -42.599 1.00 0.00
ATOM 4159 O VAL 276 -36.356 3.429 -43.629 1.00 0.00
ATOM 4160 OXT VAL 276 -35.893 4.969 -42.117 1.00 0.00
TER
ATOM 4161 N VAL 277 23.085 12.972 28.434 1.00 0.00
ATOM 4162 H1 VAL 277 22.569 12.074 28.339 1.00 0.00
--
ATOM 6237 HG23 VAL 414 35.856 26.087 41.081 1.00 0.00
ATOM 6238 C VAL 414 36.634 28.017 42.599 1.00 0.00
ATOM 6239 O VAL 414 36.356 27.360 43.629 1.00 0.00
ATOM 6240 OXT VAL 414 35.893 28.900 42.117 1.00 0.00
TER
ATOM 6241 N VAL 415 16.670 12.972 -28.434 1.00 0.00
ATOM 6242 H1 VAL 415 17.186 12.074 -28.339 1.00 0.00
--
ATOM 8317 HG23 VAL 552 3.899 26.087 -41.081 1.00 0.00
ATOM 8318 C VAL 552 3.121 28.017 -42.599 1.00 0.00
ATOM 8319 O VAL 552 3.399 27.360 -43.629 1.00 0.00
ATOM 8320 OXT VAL 552 3.862 28.900 -42.117 1.00 0.00
TER
ATOM 8321 Na+ Na+ 553 47.181 -19.633 -3.982 1.00 0.00
TER
ATOM 8322 Na+ Na+ 554 3.946 -25.853 -10.784 1.00 0.00
TER
ATOM 8323 Na+ Na+ 555 -50.408 26.517 14.763 1.00 0.00
TER
ATOM 8324 Na+ Na+ 556 -14.949 -8.966 -31.398 1.00 0.00
TER
ATOM 8325 Na+ Na+ 557 -15.589 -3.013 -37.197 1.00 0.00
TER
ATOM 8326 Na+ Na+ 558 38.640 -15.080 50.091 1.00 0.00
TER
ATOM 8327 Na+ Na+ 559 -15.149 -8.631 49.773 1.00 0.00
TER
ATOM 8328 Na+ Na+ 560 40.719 34.627 7.402 1.00 0.00
TER
ATOM 8329 Na+ Na+ 561 -28.126 30.960 5.551 1.00 0.00
TER
ATOM 8330 Na+ Na+ 562 35.619 -2.185 11.162 1.00 0.00
TER
ATOM 8331 Na+ Na+ 563 -2.874 21.675 -15.633 1.00 0.00
TER
ATOM 8332 Na+ Na+ 564 57.586 -5.895 49.164 1.00 0.00
TER
ATOM 8333 Na+ Na+ 565 -27.107 21.611 7.506 1.00 0.00
TER
ATOM 8334 Na+ Na+ 566 -7.431 -24.136 -10.510 1.00 0.00
TER
ATOM 8335 Na+ Na+ 567 40.804 -24.618 24.053 1.00 0.00
TER
ATOM 8336 Na+ Na+ 568 -15.058 -20.022 -22.262 1.00 0.00
TER
ATOM 8337 Na+ Na+ 569 -55.537 -26.315 -3.550 1.00 0.00
TER
ATOM 8338 Na+ Na+ 570 17.374 -9.138 8.193 1.00 0.00
TER
ATOM 8339 Na+ Na+ 571 10.786 7.946 14.537 1.00 0.00
TER
ATOM 8340 Na+ Na+ 572 25.211 -9.487 31.627 1.00 0.00
TER
ATOM 8341 Na+ Na+ 573 -3.738 -11.365 -19.198 1.00 0.00
TER
ATOM 8342 Na+ Na+ 574 40.738 18.775 -41.015 1.00 0.00
TER
ATOM 8343 Na+ Na+ 575 -55.892 26.840 31.042 1.00 0.00
TER
ATOM 8344 Na+ Na+ 576 -9.703 15.488 11.456 1.00 0.00
TER
ATOM 8345 Na+ Na+ 577 -57.016 0.302 50.828 1.00 0.00
TER
ATOM 8346 Na+ Na+ 578 37.543 30.856 -1.666 1.00 0.00
TER
ATOM 8347 Na+ Na+ 579 40.813 27.138 -22.923 1.00 0.00
TER
ATOM 8348 Na+ Na+ 580 -2.748 17.077 11.736 1.00 0.00
TER
ATOM 8349 O WAT 581 26.427 1.690 7.272 1.00 0.00
ATOM 8350 H1 WAT 581 25.681 1.214 7.738 1.00 0.00
ATOM 8351 H2 WAT 581 27.226 1.724 7.872 1.00 0.00
TER
ATOM 8352 O WAT 582 50.214 -19.403 -51.170 1.00 0.00
ATOM 8353 H1 WAT 582 50.180 -19.553 -52.159 1.00 0.00
ATOM 8354 H2 WAT 582 49.900 -18.477 -50.963 1.00 0.00
TER
ATOM 8355 O WAT 583 -55.075 25.518 -45.843 1.00 0.00
ATOM 8356 H1 WAT 583 -55.477 25.713 -44.949 1.00 0.00
ATOM 8357 H2 WAT 583 -54.288 24.911 -45.730 1.00 0.00
TER
ATOM 8358 O WAT 584 21.785 1.646 -46.980 1.00 0.00
ATOM 8359 H1 WAT 584 21.310 2.353 -46.457 1.00 0.00
ATOM 8360 H2 WAT 584 22.363 1.108 -46.366 1.00 0.00
TER
ATOM 8361 O WAT 585 -12.857 10.712 -43.838 1.00 0.00
ATOM 8362 H1 WAT 585 -11.898 10.432 -43.801 1.00 0.00
ATOM 8363 H2 WAT 585 -12.967 11.433 -44.523 1.00 0.00
TER
ATOM 8364 O WAT 586 -56.791 -14.426 53.394 1.00 0.00
ATOM 8365 H1 WAT 586 -56.103 -13.966 53.956 1.00 0.00
ATOM 8366 H2 WAT 586 -56.416 -15.284 53.044 1.00 0.00
TER
ATOM 8367 O WAT 587 23.832 -29.321 11.477 1.00 0.00
ATOM 8368 H1 WAT 587 23.680 -28.379 11.778 1.00 0.00
ATOM 8369 H2 WAT 587 23.223 -29.934 11.980 1.00 0.00
TER
ATOM 8370 O WAT 588 43.282 -20.239 13.531 1.00 0.00
ATOM 8371 H1 WAT 588 43.480 -19.311 13.216 1.00 0.00
ATOM 8372 H2 WAT 588 43.732 -20.898 12.928 1.00 0.00
TER
ATOM 8373 O WAT 589 -17.419 -8.307 -42.700 1.00 0.00
ATOM 8374 H1 WAT 589 -17.180 -8.501 -41.748 1.00 0.00
Patched #36 version parses it as follows
<gemmi.Chain with 138 res>
<gemmi.Chain with 138 res>
<gemmi.Chain with 138 res>
<gemmi.Chain with 138 res>
<gemmi.Chain with 1 res>
<gemmi.Chain with 1 res>
<gemmi.Chain with 1 res>
...
Probably it's not desired in other library applications since it quite different from current master:
<gemmi.Chain with 20599 res>
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sizmailov
commented on June 1, 2024
An optional parameter could be a compromise, e.g.:
gemmi.read_pdb("temp.pdb", split_chain_on_ter=True) # False by default from gemmi.
wojdyr
commented on June 1, 2024
OK, I added such an option.
from gemmi.
sizmailov
commented on June 1, 2024
Thanks for quick fix!
from gemmi.
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