[modeller_usage] How does Modeller handle multiple structures?

[Zoe Katsimitsoulia <>]

Hello everyone, 

I am very new to modelling and working a target sequence that has just
less than 27% sequence identity with another 10 proteins that have
crystal structures. My target and templates are all myosin proteins, but
from 2 different classes, since there are no crystal structures
available for my target in its same class. 
 
I have 2 concerns/queries:

1. How will modeller handle the 10 template sequences (which themselves
show a significant amount of variation at certain key positions). More
specifically, a particular area of my seq alignment may read like this:

template 1 xxxxxGxxxxxxxx
template 2 xxxxxTxxxxxxxx
template 3 xxxxxGxxxxxxxx
template 4 xxxxxGxxxxxxxx
template 5 xxxxxGxxxxxxxx
template 6 xxxxxGxxxxxxxx
template 7 xxxxxGxxxxxxxx
target     xxxxxTxxxxxxxx

In simple terms, would modeller in this case use the coord of T in the
template 2 sequence because it matches the target at that location, or
will it use G because it is predominant in the majority of the
structures? 

2. The 10 template structures I am using are themselves in different
states, for example, partially closed conformation, open, transition,
inhibitor bound, etc. Is this beneficial to building my model or more
detrimental? I am assuming the former based on the logic that the more
info I am giving to modeller, the better my model should be.
However, perhaps there is something about the way modeller works which I
have not grasped that means its actually doing more harm adding the
structures in different states?

Thanks very much in advance,

-Zoe