VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Mon Oct 19 2020 - 17:07:54 CDT

Here is an alignment proc I wrote to do the same thing as the align button
you speak of.

proc align {rmolid smolid} {
        set ref_molid $rmolid
        set sel_molid $smolid
        set numframes [molinfo $sel_molid get numframes]
        set ref_frame [atomselect $ref_molid "protein and name CA" frame 0]
        set n 1
        set sys [atomselect $sel_molid all]
        for {set i 0} {$i < $numframes} {incr i} {
                animate goto $i
                set align_frame [atomselect $sel_molid "protein and name
CA"]
                set trans_matrix [measure fit $align_frame $ref_frame]
                $sys move $trans_matrix
                if {($n % 100) == 0 } {
                        puts "alignment $n of $numframes"
                }
                incr n
        }
        puts "Alignments complete, ready for RMSD calculations"
}

On Mon, Oct 19, 2020 at 2:46 PM Daniel STERBULEAC <daniel.sterbuleac_at_usm.ro>
wrote:

> Greetings!
>
> I am having a hard time deciphering the script behind VMD's RMSD
> visualizer tool ALIGN button. I tried using the scripts found at
> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-3497/rmsd.tcl
> but they do seem to perform different calculations.
>
> I would be grateful if anyone could help me with the script or other
> advice.
>
> All the best,
>
> Daniel
>
> ---------------
> Daniel Sterbuleac, PhD
> Assistant Professor, Stefan cel Mare University of Suceava, Romania
> Str. Universitatii, 13, Suceava
>