VMD-L Mailing List

From: Daniel STERBULEAC (daniel.sterbuleac_at_usm.ro)
Date: Mon Oct 19 2020 - 17:42:41 CDT

Dear Bassam,
that is exactly what I was looking for. I slightly modified it and compared
the output, it is precisely the same as the align button.

Appreciate it, Cheers!

All the best,
Daniel

On Tue, Oct 20, 2020 at 1:08 AM Bassam Haddad <bhaddad_at_pdx.edu> wrote:

> 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
>>
>