[modeller_usage] Syntax errors in defining model atoms
To:
Subject: [modeller_usage] Syntax errors in defining model atoms
From:
Date: Sun, 06 Jan 2013 23:09:58 +0200
Dear all,
I am trying to create distance restraints in a model based on an
example script from the modeller manual named model-addrsr.py . I am
following the exact same syntax of this script, yet I need to change
the numbering of my residues (since my restraints are for a model that
starts at residue 2 and not 1) so I add another restraint to renumber
it (self.rename_segments), however, when I try to use my new script
(listed at the bottom of this mail), I get an error message that the
atom I listed OG1:132A:A does not exist: 'No such atom: OG1:132A:A',
does anyone know what am I doing wrong here?
Thank you,
Doran
My script:
# Homology modeling by the automodel class
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ(rand_seed = -500) # create a new
MODELLER environment to build this model in
env.io.atom_files_directory = './:' # directories for input atom files
env.io.hetatm = True # read HETATM records (for Na ions)
################################
# define the modeling parameters
class mymodel(automodel):
def special_restraints(self, aln):
self.rename_segments (segment_ids=('A'),renumber_residues=(2))
rsr = self.restraints
at = self.atoms