[modeller_usage] Using of a template with the coordinates of the Calpha atoms only.
Subject: [modeller_usage] Using of a template with the coordinates of the Calpha atoms only.
From: Jean-Paul Becker <>
Date: Tue, 14 Oct 2008 10:49:06 +0200 (CEST)
Dear Modeller users,
I constructed a model of a protein using a template which contains
only the Calpha trace.
Due to a question of a reviewer of the article i submitted for publication, i
am seeking for precisions on how the Calpha trace is rebuilt to atomic
resolution and then made into the model.
I guess these steps are performed by the functions:
model.generate_topology() and/or Restraints.make(),
but i do not understand how modeller generates all the essential
restraints to build the model when almost all the atoms of the template
are missing except the Calpha.
Does these restraints come from a library ?
In this case, how is this library built ?
I did not mange to find many details concerning this point
in the manual, so i would really appreciate if anyone could
give me some explanations.
Many thanks in advance for your time and knowledge.
Structure et Fonction des Membranes Biologiques (SFMB)
Centre de Biologie Structurale et de Bioinformatique (CBSB)
Faculté des Sciences
Université Libre de Bruxelles
Campus de la Plaine
Boulevard du Triomphe