Subject: Re: [modeller_usage] grid_search and hetatm
From: Modeller Caretaker <>
Date: Thu, 21 Dec 2017 10:14:00 -0800
On 12/21/17 1:36 AM, Carlo Camilloni wrote:
I am fitting a protein with cofactors in a cryo-em density using
grid_search. It works but the fitted structure does’t include anymore
the HETATM fields with the cofactors.
My input looks
env = environ()
env.io.hetatm = True
env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology
env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters
Is this something that is not supported or I am doing something wrong?
Looking at the code, it should be supported (although I don't think it's
ever been tested - it's debatable whether the fit of the cofactors into
the density is handled correctly). But you've asked the algorithm to
read a single chain from 'struct' (chains_num=). I don't see your PDB
file, but maybe the cofactors are in a different chain?