PDBWriter writes some C as Ca and some N as Na #2732
Description
Expected behavior
I expect PDBWriter to correctly write C and N atoms.
Actual behavior
Some C atoms are written as Ca and some N atoms are written as Na. I think the writer is using the old instead of the new elements attribute (see #2647 and #2648).
Code to reproduce the behavior
The following PDB file is the ligand in 3MXF
HETATM 1076 CAA JQ1 A 1 29.899 18.962 1.724 1.00 7.28 C
HETATM 1077 CAB JQ1 A 1 25.204 15.116 1.393 1.00 9.95 C
HETATM 1078 CAC JQ1 A 1 25.682 14.930 -1.694 1.00 10.30 C
HETATM 1079 CAD JQ1 A 1 29.233 13.118 -5.465 1.00 15.92 C
HETATM 1080 CAE JQ1 A 1 30.649 11.124 -4.687 1.00 18.36 C
HETATM 1081 CAF JQ1 A 1 28.543 11.742 -3.510 1.00 15.62 C
HETATM 1082 OAG JQ1 A 1 32.109 13.864 -4.714 1.00 20.67 O
HETATM 1083 CLAH JQ1 A 1 24.824 18.476 -6.770 1.00 9.02 CL
HETATM 1084 CAI JQ1 A 1 25.532 17.964 -4.219 1.00 8.34 C
HETATM 1085 CAJ JQ1 A 1 27.032 17.110 -5.868 1.00 6.71 C
HETATM 1086 CAK JQ1 A 1 26.351 17.447 -3.210 1.00 6.66 C
HETATM 1087 CAL JQ1 A 1 27.857 16.609 -4.867 1.00 6.48 C
HETATM 1088 CAM JQ1 A 1 31.898 14.964 -2.576 1.00 8.11 C
HETATM 1089 NAN JQ1 A 1 29.662 16.042 -2.828 1.00 7.69 N
HETATM 1090 NAO JQ1 A 1 31.817 18.128 0.283 1.00 8.44 N
HETATM 1091 NAP JQ1 A 1 32.044 17.250 -0.625 1.00 8.68 N
HETATM 1092 OAQ JQ1 A 1 30.400 13.247 -3.384 1.00 10.41 O
HETATM 1093 SAR JQ1 A 1 27.810 16.331 1.456 1.00 8.19 S
HETATM 1094 CAS JQ1 A 1 31.475 13.972 -3.665 1.00 13.62 C
HETATM 1095 CAT JQ1 A 1 28.375 16.220 -2.489 1.00 7.13 C
HETATM 1096 CAU JQ1 A 1 25.880 17.822 -5.542 1.00 8.01 C
HETATM 1097 CAV JQ1 A 1 30.534 18.050 0.671 1.00 7.28 C
HETATM 1098 CAW JQ1 A 1 27.522 16.765 -3.512 1.00 6.19 C
HETATM 1099 CAX JQ1 A 1 26.460 15.625 0.646 1.00 7.78 C
HETATM 1100 CAY JQ1 A 1 26.696 15.557 -0.722 1.00 7.26 C
HETATM 1101 CAZ JQ1 A 1 30.894 16.581 -0.833 1.00 7.50 C
HETATM 1102 CBA JQ1 A 1 27.931 16.125 -1.137 1.00 8.00 C
HETATM 1103 CBB JQ1 A 1 28.660 16.602 -0.030 1.00 6.74 C
HETATM 1104 CBC JQ1 A 1 30.646 15.463 -1.866 1.00 9.05 C
HETATM 1105 NBD JQ1 A 1 29.932 17.088 -0.061 1.00 7.77 N
HETATM 1106 CBE JQ1 A 1 29.731 12.302 -4.299 1.00 14.82 C
Some C atoms have an atom type that contains CA and some N atoms have an atom type that contains NA (see #1808).
The PDB file written out by the following code is wrong:
In [1]: import MDAnalysis as mda
In [2]: mda.__version__
Out[2]: '0.20.2-dev0'
In [3]: u = mda.Universe("3MXF.pdb")
In [4]: sel = u.select_atoms("not protein and not resname HOH")
In [5]: sel
Out[5]: <AtomGroup with 31 atoms>
In [6]: sel.write("3MXF_out.pdb")Wrong output:
HEADER
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 CAA JQ1 A 1 29.899 18.962 1.724 1.00 7.28 A C
ATOM 2 CAB JQ1 A 1 25.204 15.116 1.393 1.00 9.95 A C
ATOM 3 CAC JQ1 A 1 25.682 14.930 -1.694 1.00 10.30 A C
ATOM 4 CAD JQ1 A 1 29.233 13.118 -5.465 1.00 15.92 A C
ATOM 5 CAE JQ1 A 1 30.649 11.124 -4.687 1.00 18.36 A C
ATOM 6 CAF JQ1 A 1 28.543 11.742 -3.510 1.00 15.62 A C
ATOM 7 OAG JQ1 A 1 32.109 13.864 -4.714 1.00 20.67 A O
ATOM 8 CLAH JQ1 A 1 24.824 18.476 -6.770 1.00 9.02 A CL
ATOM 9 CAI JQ1 A 1 25.532 17.964 -4.219 1.00 8.34 A C
ATOM 10 CAJ JQ1 A 1 27.032 17.110 -5.868 1.00 6.71 A C
ATOM 11 CAK JQ1 A 1 26.351 17.447 -3.210 1.00 6.66 A C
ATOM 12 CAL JQ1 A 1 27.857 16.609 -4.867 1.00 6.48 A CA
ATOM 13 CAM JQ1 A 1 31.898 14.964 -2.576 1.00 8.11 A C
ATOM 14 NAN JQ1 A 1 29.662 16.042 -2.828 1.00 7.69 A NA
ATOM 15 NAO JQ1 A 1 31.817 18.128 0.283 1.00 8.44 A NA
ATOM 16 NAP JQ1 A 1 32.044 17.250 -0.625 1.00 8.68 A NA
ATOM 17 OAQ JQ1 A 1 30.400 13.247 -3.384 1.00 10.41 A O
ATOM 18 SAR JQ1 A 1 27.810 16.331 1.456 1.00 8.19 A S
ATOM 19 CAS JQ1 A 1 31.475 13.972 -3.665 1.00 13.62 A C
ATOM 20 CAT JQ1 A 1 28.375 16.220 -2.489 1.00 7.13 A C
ATOM 21 CAU JQ1 A 1 25.880 17.822 -5.542 1.00 8.01 A C
ATOM 22 CAV JQ1 A 1 30.534 18.050 0.671 1.00 7.28 A C
ATOM 23 CAW JQ1 A 1 27.522 16.765 -3.512 1.00 6.19 A C
ATOM 24 CAX JQ1 A 1 26.460 15.625 0.646 1.00 7.78 A C
ATOM 25 CAY JQ1 A 1 26.696 15.557 -0.722 1.00 7.26 A C
ATOM 26 CAZ JQ1 A 1 30.894 16.581 -0.833 1.00 7.50 A C
ATOM 27 CBA JQ1 A 1 27.931 16.125 -1.137 1.00 8.00 A C
ATOM 28 CBB JQ1 A 1 28.660 16.602 -0.030 1.00 6.74 A C
ATOM 29 CBC JQ1 A 1 30.646 15.463 -1.866 1.00 9.05 A C
ATOM 30 NBD JQ1 A 1 29.932 17.088 -0.061 1.00 7.77 A N
ATOM 31 CBE JQ1 A 1 29.731 12.302 -4.299 1.00 14.82 A BE
END
Current version of MDAnalysis
- Which version are you using?
0.20.2-dev0 - Which version of Python (
python -V)?3.7. - Which operating system?
macOS 10.15.5/Ubuntu 18.04