Re: [modeller_usage] constant starting molecule for models
To: Dermot Mallon <>
Subject: Re: [modeller_usage] constant starting molecule for models
From: Modeller Caretaker <>
Date: Thu, 06 Jun 2013 10:36:53 -0700
Cc:
On 6/6/13 4:00 AM, Dermot Mallon wrote:
Between models with
identical sequence the RMSD is ~0.2
This is expected behavior. Modeller models are samples from the set of
all models that satisfy the restraints.
Therefore, I wonder if there is a way to ask modeller to start at the
same point in these molecules? I tried a.rand_model = None, but that
doesn't appear to be the correct option.
It sounds like what you're looking for is rand_method, not rand_model.
But Modeller will still optimize to satisfy the restraints, which will
move things around. You could just take the initial model (the *.ini
file) which is a PDB file of the model before randomization and
optimization. This won't change unless you change your alignment and/or
template structures. But since it's unoptimized it could contain clashes.