Re: [modeller_usage] Error: No atoms were read from the specified input PDB file
To: Ann Spevacek <>
Subject: Re: [modeller_usage] Error: No atoms were read from the specified input PDB file
From: Modeller Caretaker <>
Date: Wed, 17 Nov 2010 11:31:48 -0800
Cc:
On 11/03/2010 02:57 PM, Ann Spevacek wrote:
I am trying to align two models, one an NMR structure (1XYX.pdb) and
one a simulation (frame100.pdb) and I get the following error:
No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in
MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " FIRST",
chain " A";
atom file name: ./frame100.pdb
OK, so you have asked Modeller to read coordinates from the
"frame100.pdb" PDB file, starting at the first residue in the A chain.
This is what the frame100.pdb file looks like:
There is no "A" chain in this PDB file... so how will Modeller be able
to read it?
And this is the salign.py file that I am trying to use:
# Illustrates the SALIGN multiple structure/sequence alignment
from modeller import *
log.verbose()
env = environ()
env.io.atom_files_directory = './:../atom_files/'
aln = alignment(env)
for (code, chain) in (('1XYX', 'A'), ('frame100', 'A')):
Replace the second 'A' with '', to read from a chain with no ID, as in
your PDB file.