Manipulating residues on the protein surface - VMD

Written by Super User. Posted in Uncategorised

Currently, I am trying to determine the "correct" protonation state of a protein after ESI ionization. For that, I have to consider that protons are mobile on the protein's surface. In order to select (and write as  separate pdb file for example) residues with a solvent-accessible surface of bigger than 20 square-Angstrom I use the following tcl script:

set allsel [atomselect top all]
set residlist [lsort -unique -integer [$allsel get resid]]
puts residlist
set selectlist {}
foreach r $residlist {
set selres [atomselect top "resid $r" ]
set rSASA [measure sasa 2.0 $allsel -restrict $selres]  
if {$rSASA > 20} {
        lappend selectlist $r
        puts $r
mol representation "VDW"
mol color "Colorid 4"
mol selection resid $selectlist    
mol addrep 0