Re: [modeller_usage] Fibrillar collagen structure model 3hr2 Inbox
To: Amadeus Cavalcanti Salvador de Alcântara <>,
Subject: Re: [modeller_usage] Fibrillar collagen structure model 3hr2 Inbox
From: Modeller Caretaker <>
Date: Wed, 27 Jan 2021 15:39:31 -0800
On 1/27/21 1:48 PM, Amadeus Cavalcanti Salvador de Alcântara wrote:
The 3hr2.pdb contains 2 non standard amino acids:
HYP hydroxyproline
LYZ Hydroxylysine
I would be inclined to edit the PDB file and replace the coordinates for
these modified residues with the corresponding standard amino acids. You
can certainly use the '.' residue type, and treat them as ligands, but
that will simply copy them from target to template, allowing no
relaxation (or mutation), usually not what you want for modified residues.
The model looks good, however, it is not as close to the 3hr2 structured
as I wished. As a mechanical engineer I am no used to those models nor
to homology modeling and have been learning all here by reading the
manual, instructions and mail listing. Did I make many/any mistakes?
Where and what? Can the model become better (more close to the 3hr2
template structure)? If yes, how?
Modeller builds models that resemble the template, by construction. If
you're seeing a big divergence, you likely have an alignment error. You
should carefully inspect the alignment and look for obvious problems,
such as lots of gaps, sequences of different lengths, or gaps in regions
of known secondary structure.
How to know if a model is "good enough"?
This depends on what you want to use it for. But DOPE is only a ranking
- it doesn't tell you how "good" the model is, only whether it's better
than your other models. A score like normalized DOPE or TSVMod would
give you a better idea; these can be calculated at