ExtractHeteroAtoms returns empty heteroatom file

BioBB
1

I’m following the protein ligand tutorial with my own files.

I used ExtractHeteroAtoms but got an empty file for the output_heteroatom_path option.

input:
prop = {
‘heteroatoms’ : [{“name”: “LIG”}]

ExtractHeteroAtoms(input_structure_path=‘eic-mol1.pdb’,
output_heteroatom_path=ligandFile,
properties=prop).launch()

output:
1.pdb loaded
Title:
Experimental method: unknown
Resolution: 0.0 A

Num. models: 1
Num. chains: 1 ( : Protein)
Num. residues: 314
Num. residues with ins. codes: 0
Num. HETATM residues: 1
Num. ligands or modified residues: 1
Num. water mol.: 0
Num. atoms: 4917
Modified residues found
LIG 314

Step 1: ligands --remove All

Running ligands. Options: --remove All
1 Ligands detected
LIG 314
Ligands removed All (1)

ExtractProtein works correctly and returns just the protein file.

Thank you,

Dan

2

Hi, can you provide the 1.pdb file?

Thanks

3

Hi Genis,

Here is the file.
eic-mol1.pdb (394.6 KB)

Thank you,

Dan

4

Hi Dan,

There was a bug in the code and it didn’t work properly with PDB files without chain. I’ve fixed it and it will be available in the next release. In the meantime, please add a chain to your PDB file and it will work.

Adding the chain only to the HETATM lines will do the trick:

HETATM 4915 N LIG A 314 -15.104 -1.492 -11.854 0.00 0.00 N
HETATM 4916 C LIG A 314 -15.529 -0.853 -13.110 0.00 0.00 C
HETATM 4917 C LIG A 314 -15.666 0.665 -12.891 0.00 0.00 C
HETATM 4918 C LIG A 314 -15.147 1.646 -13.734 0.00 0.00 C
HETATM 4919 C LIG A 314 -15.497 2.853 -13.170 0.00 0.00 C
HETATM 4920 C LIG A 314 -16.209 2.544 -12.014 0.00 0.00 C
HETATM 4921 C LIG A 314 -16.756 3.484 -11.130 0.00 0.00 C
HETATM 4922 C LIG A 314 -17.784 3.107 -10.255 0.00 0.00 C
HETATM 4923 C LIG A 314 -18.331 4.047 -9.371 0.00 0.00 C
HETATM 4924 C LIG A 314 -17.849 5.364 -9.362 0.00 0.00 C
HETATM 4925 C LIG A 314 -16.821 5.741 -10.237 0.00 0.00 C
HETATM 4926 C LIG A 314 -16.274 4.801 -11.121 0.00 0.00 C
HETATM 4927 O LIG A 314 -16.294 1.230 -11.874 0.00 0.00 O
HETATM 4928 F LIG A 314 -18.376 6.269 -8.510 0.00 0.00 F
HETATM 4929 H01 LIG A 314 -15.126 -0.821 -11.115 0.00 0.00 H

Thanks!

5

Cool - Thank you!