load and display protein structure

[Lili-Cao]

I get a lot of warning like WARNING: not removing hydrogen atom without neighbors

the protein_file file are from maestro in pdb format

u = mda.Universe(protein_file)
protein_mol = plf.Molecule.from_mda(u)
plf.display_residues(protein_mol)

May I ask why the display function cannot show the residues?

[cbouy]

Hi,

Most likely the pdb file contains the CONECT record for bonds only for a few non standard residues or small molecules, so since there are bonds MDAnalysis will not try to guess the missing ones.
Try loading the file with mda.Universe(protein_file, guess_bonds=True) or have Maestro export all bonds

[Lili-Cao]

Hi,

Yes you are right, the connect info is not for all bonds.
I tried with guess_bond and now its much better.

Thank you!