VMD-L Mailing List
From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Mon Oct 19 2020 - 17:07:54 CDT
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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
>
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