Subject: Re: [modeller_usage] Quick Question on Automodel
From: Modeller Caretaker <>
Date: Mon, 1 Mar 2021 10:42:21 -0800
On 2/28/21 1:00 PM, Pedro Guillem wrote:
I'm trying to model from a known template (ident 37%).
The template is missing the first 3 residues in the structure.
- I start reading the template at position 4.
- I add 3 dashes to the beginning of the template to compensate for the
missing residues. (otherwise I get a "residue mismatch" error from modeller)
Dashes/gaps do not have any effect on which residues are read from the
PDB file; this is controlled entirely by the PIR header (the line
starting with "structureX", where you - apparently correctly - have 4 as
the start residue number). Dashes/gaps only control the correspondence
between target and template residues.
Here is a bit of my ali file. I want the TRL of the template to align
with the TRM of the sequence.
Your alignment looks fine to me, assuming by "..." you mean "the rest of
the sequence goes here". (A literal "." has a special meaning to
Modeller; read in the manual about modeling with ligands.)
When it finishes, the position of TRM has a different offset in relation
to TRL
Not sure what you mean here, unless you were expecting T to be numbered
4. Modeller numbers residues in your model starting from 1, regardless
of your alignment. If you want a different numbering, use
rename_segments(); see