[modeller_usage] initial model

Hello All,

I want to model a multi-domain protein. Thus, I aligned manually all templates (corresponding to the individual domains) and used them as an input for Modeller. (Note that the templates overlap only over few residues.)

However, when I compared the initial model (.ini) to the aligned templates, I saw that Modeller did something more than just transferring the coordinates from the templates. Namely, the relative orientation of domains is not as in my structural alignment. Is thee any way to force Modeller to use exactly the input coordinates?

initial_malign3d is set to False and default transfer_xyz() is used

Thanks for help! Staszek