I found the following issue with this use case: I'd like to extract a single model from a structure that has multiple ones as a pdb file.
Expected behaviour
The output files keeps the information of HETATM and ATOM records
HETATM 1 C FVA A 1 -3.595 0.079 3.555 1.00 0.00 C
HETATM 2 N FVA A 1 -2.330 -0.205 1.496 1.00 0.00 N
HETATM 3 O FVA A 1 -3.911 -1.055 3.906 1.00 0.00 O
HETATM 4 CA FVA A 1 -3.501 0.435 2.070 1.00 0.00 C
HETATM 5 CB FVA A 1 -4.752 0.042 1.281 1.00 0.00 C
HETATM 6 CG1 FVA A 1 -5.974 0.826 1.764 1.00 0.00 C
HETATM 7 CG2 FVA A 1 -4.535 0.232 -0.221 1.00 0.00 C
HETATM 8 O1 FVA A 1 -1.445 1.720 0.692 1.00 0.00 O
HETATM 9 CN FVA A 1 -1.409 0.501 0.859 1.00 0.00 C
ATOM 10 N GLY A 2 -3.315 1.072 4.387 1.00 0.00 N
ATOM 11 CA GLY A 2 -3.364 0.879 5.826 1.00 0.00 C
ATOM 12 C GLY A 2 -2.503 1.917 6.549 1.00 0.00 C
ATOM 13 O GLY A 2 -3.009 2.947 6.992 1.00 0.00 O
ATOM 14 N ALA A 3 -1.218 1.610 6.645 1.00 0.00 N
ATOM 15 CA ALA A 3 -0.282 2.504 7.305 1.00 0.00 C
ATOM 16 C ALA A 3 1.118 2.286 6.729 1.00 0.00 C
ATOM 17 O ALA A 3 1.488 1.161 6.395 1.00 0.00 O
ATOM 18 CB ALA A 3 -0.333 2.271 8.817 1.00 0.00 C
Actual behaviour
All atom coordinates are written as ATOM records
ATOM 1 C FVA A 1 -3.595 0.079 3.555 1.00 0.0 C
ATOM 2 N FVA A 1 -2.330 -0.205 1.496 1.00 0.0 N
ATOM 3 O FVA A 1 -3.911 -1.055 3.906 1.00 0.0 O
ATOM 4 CA FVA A 1 -3.501 0.435 2.070 1.00 0.0 C
ATOM 5 CB FVA A 1 -4.752 0.042 1.281 1.00 0.0 C
ATOM 6 CG1 FVA A 1 -5.974 0.826 1.764 1.00 0.0 C
ATOM 7 CG2 FVA A 1 -4.535 0.232 -0.221 1.00 0.0 C
ATOM 8 O1 FVA A 1 -1.445 1.720 0.692 1.00 0.0 O
ATOM 9 CN FVA A 1 -1.409 0.501 0.859 1.00 0.0 C
ATOM 10 N GLY A 2 -3.315 1.072 4.387 1.00 0.0 N
ATOM 11 CA GLY A 2 -3.364 0.879 5.826 1.00 0.0 C
ATOM 12 C GLY A 2 -2.503 1.917 6.549 1.00 0.0 C
ATOM 13 O GLY A 2 -3.009 2.947 6.992 1.00 0.0 O
ATOM 14 N ALA A 3 -1.218 1.610 6.645 1.00 0.0 N
ATOM 15 CA ALA A 3 -0.282 2.504 7.305 1.00 0.0 C
ATOM 16 C ALA A 3 1.118 2.286 6.729 1.00 0.0 C
ATOM 17 O ALA A 3 1.488 1.161 6.395 1.00 0.0 O
ATOM 18 CB ALA A 3 -0.333 2.271 8.817 1.00 0.0 C
Example code to reproduce
import atomium
structure = atomium.fetch("1GRM")
mod = structure.models[0]
mod.save("1GRM_model1.pdb")
Hey, first of all thanks for this great tool.
I found the following issue with this use case: I'd like to extract a single model from a structure that has multiple ones as a pdb file.
Expected behaviour
The output files keeps the information of HETATM and ATOM records
Actual behaviour
All atom coordinates are written as ATOM records
Example code to reproduce
Then compare with https://files.rcsb.org/view/1GRM.pdb
Python Version/Operating System
Python 3.6, atomium 1.0.7