NGL can't show water for this file

[hainm]

Hi

NGL (2.2.2 and even older) can't show the pdb below (no waters are shown)

TITLE     MDANALYSIS FRAME 0: Created by PDBWriter
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
REMARK     285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET
REMARK     285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION
REMARK     285 WAS MISSING.
REMARK     285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK     285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON
REMARK     285 THIS RECORD ARE MEANINGLESS.
ATOM      1  O   WAT X  10      22.587  25.626  24.025  1.00  0.00      SYST O
ATOM      2  H1  WAT X  10      21.699  25.968  23.923  1.00  0.00      SYST H
ATOM      3  H2  WAT X  10      22.871  25.427  23.133  1.00  0.00      SYST H
ATOM      4  O   WAT X  11      20.550  28.227  29.909  1.00  0.00      SYST O
ATOM      5  H1  WAT X  11      21.122  27.459  29.909  1.00  0.00      SYST H
ATOM      6  H2  WAT X  11      20.550  28.526  29.000  1.00  0.00      SYST H
ATOM      7  O   WAT X  12      30.408  37.046  27.764  1.00  0.00      SYST O
ATOM      8  H1  WAT X  12      29.789  37.502  27.193  1.00  0.00      SYST H
ATOM      9  H2  WAT X  12      31.263  37.201  27.363  1.00  0.00      SYST H
ATOM     10  O   WAT X  13      29.602  33.030  29.370  1.00  0.00      SYST O
ATOM     11  H1  WAT X  13      29.533  32.089  29.209  1.00  0.00      SYST H
ATOM     12  H2  WAT X  13      30.364  33.120  29.943  1.00  0.00      SYST H
CONECT    1    2    3
CONECT    2    1    3
CONECT    3    1    2
CONECT    4    5    6
CONECT    5    4    6
CONECT    6    4    5
CONECT    7    8    9
CONECT    8    7    9
CONECT    9    7    8
CONECT   10   11   12
CONECT   11   10   12
CONECT   12   10   11
END

The file is shown fine with Maestro program

[ppillot]

The SYST part does not look standard to me

Le dim. 14 janv. 2024 à 20:09, Hai Nguyen @.***> a écrit :

Hi

NGL (2.2.2 and even older) can't show file (no waters are shown)

TITLE MDANALYSIS FRAME 0: Created by PDBWriter CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION REMARK 285 WAS MISSING. REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON REMARK 285 THIS RECORD ARE MEANINGLESS. ATOM 1 O WAT X 10 22.587 25.626 24.025 1.00 0.00 SYST O ATOM 2 H1 WAT X 10 21.699 25.968 23.923 1.00 0.00 SYST H ATOM 3 H2 WAT X 10 22.871 25.427 23.133 1.00 0.00 SYST H ATOM 4 O WAT X 11 20.550 28.227 29.909 1.00 0.00 SYST O ATOM 5 H1 WAT X 11 21.122 27.459 29.909 1.00 0.00 SYST H ATOM 6 H2 WAT X 11 20.550 28.526 29.000 1.00 0.00 SYST H ATOM 7 O WAT X 12 30.408 37.046 27.764 1.00 0.00 SYST O ATOM 8 H1 WAT X 12 29.789 37.502 27.193 1.00 0.00 SYST H ATOM 9 H2 WAT X 12 31.263 37.201 27.363 1.00 0.00 SYST H ATOM 10 O WAT X 13 29.602 33.030 29.370 1.00 0.00 SYST O ATOM 11 H1 WAT X 13 29.533 32.089 29.209 1.00 0.00 SYST H ATOM 12 H2 WAT X 13 30.364 33.120 29.943 1.00 0.00 SYST H CONECT 1 2 3 CONECT 2 1 3 CONECT 3 1 2 CONECT 4 5 6 CONECT 5 4 6 CONECT 6 4 5 CONECT 7 8 9 CONECT 8 7 9 CONECT 9 7 8 CONECT 10 11 12 CONECT 11 10 12 CONECT 12 10 11 END

The file is shown fine with Maestro program image.png (view on web) https://github.com/nglviewer/ngl/assets/4451957/86ad9964-e7ad-430b-9572-7377ab033170

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[hainm]

The SYST part does not look standard to me

@ppillot I see.

For the record: mostar could show the file too

[ppillot]

Can you check that after recentring and choosing "water" instead of "ligand" for the ball+stick representation, the water molecules are displayed:

[hainm]

wonderful. I confirm that. Thanks @ppillot as usual.