Script to add linker region between two PDB structures.

[Andrew Orry]

Here is a script to add a linker region between two PDB structures. 

# copy and paste into the terminal window

# in this example the first object is an nmr model so we just want the first conformation

TOOLS.pdbReadNmrModels="first"  

# read in the PDB files

read pdb "2L00"

read pdb "2xe0"

# delete everything except for the first subunit in each pdb or the subunit you want to join by a linker 

delete a_2L00.!a

delete a_2xe0.!a

# make a 3D peptide of 2xe0 and 2l00 with the linker sequence in between. In this example we have used 5 times Ala (AAAAA)

build string IcmSequence( Sequence( a_2.1  )//Sequence("AAAAA")//Sequence( a_1.1  ) )

 

# now we are going to thread the peptide onto the pdb structure of 2L00

set tether align a_ a_1.1

 minimize tether

delete tether

# now we are going to thread the rest of the peptide onto the strcutrre of 2xe0

 set tether align a_ a_2.1

 minimize tether

# now we are going to optimize the linker region

vwMethod = "soft"

minimize v_/153:157

# assign secondary structure

assign sstructure a_def.a1

# display molecule

ds ribbon a_def.a1