Structure Alignment with VMD

Written by Super User. Posted in Uncategorised

In a current side-project, I need to align some structural models of an elongated monomer protein to the crystallographically solved dimer structure. The task is to align each fragment (and the additional residues) to a chain in the dimer. Loading the respective structures in VMD looks like this


To perform the alignment despite additional residues and atom ordering, it is important to inspect the pdb files and identify the regions of sequence identity. Then only Calpha carbons are used to determine the transformation matrix to best fit chain A or chain B. Finally the transformation is applied to the whole monomer. Coordinates are written as pdb files that are easily merged by hand to obtain the full pdb file.

In the example (PDB 1BG8) there are 615 atoms in each chain. In the elongated (homology modelling of the flexible Nterminal residues not solved in Xray) fragment the sequence identity with the chains of 1BG8 is found in the range of atoms 55 to 666. The selection and transformation can be easily done using the tcl interface of VMD:

i loaded 1 unit of 1BG8 and 2 fragments of the elongated monomer with ID's 0, 1 and 2

set sel0 [atomselect 0 {{serial 1 to 615} and name CA }]
set sel1 [atomselect 0 {{serial 616 to 1230} and name CA }]
set sel2 [atomselect 1 {{serial 55 to 666} and name CA }]
set M1 [measure fit $sel2 $sel0]
set M2 [measure fit $sel2 $sel1]
set sel3 [atomselect 1 all]
set sel4 [atomselect 2 all]
$sel3 move $M1
$sel4 move $M2

the result is -  as expected - aligned