Aligning hexameric proteins along an axis

This tcl script aligns a hexamer such that its central axis is aligned along the y-axis.


set all [atomselect top protein]
$all moveby [vecscale [measure center $all] -1]

set res10 [atomselect top "resid 10"]
set res40 [atomselect top "resid 40"]

set cenres10 [measure center $res10]
set cenres40 [measure center $res40]

set vector [vecsub $cenres10 $cenres40]

$all move [transvecinv $vector]
$all move [transaxis z 90]

foreach i {A B C D E F} {
        set chain [atomselect top "chain $i and protein and resid 4 to 105"]
        $chain writepdb chain$i.pdb
}

This script is also applicable to trimers, tetramers and other aggregates that have a well defined central axis.