Re: [modeller_usage] using DSS/BS crosslink information as restrain
To: thereal sisterdot <>,
Subject: Re: [modeller_usage] using DSS/BS crosslink information as restrain
From: Modeller Caretaker <>
Date: Tue, 8 Sep 2015 13:03:20 -0700
On 09/07/2015 11:27 PM, thereal sisterdot wrote:
I decided to try usingupper_bound restraints as above to feed the
crosslink information to modeller.
But actually the restraints did not improve the conflicting distances.
my assumption is that the few restrains from the crosslinks can not
compete with the many restrains coming from the alignment.
I guess one would have to modify the model later somehow.
Modeller will always build a model that resembles the template (in
aligned regions) by construction - that's what it's designed to do. So
in order to satisfy your crosslinks you would have to remove the
corresponding distances from the template. One way to do this would be
to break the template into multiple pieces (e.g. one per chain or
domain), i.e. changing your alignment from
template AAAAA/BBBBB
model mmmmm/mmmmm
to
template1 AAAAA/-----
template2 -----/BBBBB
model mmmmm/mmmmm
Then you'll get no A-B interactions enforced in your model because
those chains are in different templates.