Re: [modeller_usage] Design a linker for two-domain chimeric protein
To: Чугунов Антон <>, "" <>
Subject: Re: [modeller_usage] Design a linker for two-domain chimeric protein
From: Modeller Caretaker <>
Date: Mon, 6 Apr 2020 13:15:04 -0700
On 4/4/20 9:23 AM, Чугунов Антон wrote:
I want to perform task almost as in the FAQ #1
<https://salilab.org/modeller/FAQ.html#1>: I have two separate proteins,
and want to receive one -- where these two are joined by the [G4S]n
linker. The major difference from the example in FAQ that I have the
exact orientation of both domains (they are docked onto the same
receptor at different sites), and I want them to be prohibited from
movement. The common protocol moves the downstream domain so it changes
its position and orientation, but I have to basically "freeze" the both
domains, allowing the linker to fullfill the space between them.
Either merge the two domains into one PDB file and treat them as a
single template with two chains (in which case Modeller will generate
inter-chain restraints and keep the input orientation), or deselect
those two domains so that Modeller does not refine them, as per
https://salilab.org/modeller/9.23/manual/node23.html