Re: [modeller_usage] MODELLER thinks HSEs are ATOM instead of HETATM

On 9/1/11 8:12 PM, Yingjie Lin wrote: > I ran into a problem with PDB file 1j9n, which contains HSE residues. > Each HSE line starts with "HETATM". However, when I read them into > MODELLER, > MODELLER thinks HSEs are ATOMs.

Modeller does not read the ATOM/HETATM information from PDB - it only uses it to decide which residues to read in (those marked as HETATM are only read in if you set env.io.hetatm=True).

> Where can I find MODELLER's lists/libraries of HETATM/ATOM residue types?

See modlib/restyp.lib. The first column in this file tells you whether Modeller treats a given residue type as ATOM or HETATM.

Ben Webb, Modeller Caretaker