VMD-L Mailing List

From: mish (smncbr_at_gmail.com)
Date: Tue Nov 27 2018 - 09:25:29 CST

Hi again,

I fond the issue. It was possible to assign the order {...} and then it
works fine!

Best,
Mish

On Tue, Nov 27, 2018 at 2:58 PM mish <smncbr_at_gmail.com> wrote:

> Dear all,
>
> I have a little problem when fitting a sugar ring of the resid 4 of on
> oligosaccharide over a reference frame (sugar_ring.pdb). sugar_ring.pdb
> file contants only ring atoms (C1 C2 C3 C4 C5 O5). I used
> following Tcl script to transform the trajecotry:
> ------------------------------------------------------------------
> set mol_cent [mol load pdb "sugar_ring.pdb"]
> set sel_cent [atomselect $mol_cent "all"]
> set mol [mol load netcdf "oligo.nc <http://dehydr.nc/>" parm7
> "oligo.parm7"]
> set numframes [molinfo $mol get numframes]
> for { set i 0 } { $i < $numframes } { incr i } {
> set sel [atomselect $mol "resid 4 and name C1 C2 C3 C4 C5 O5" frame $i]
> set all [atomselect $mol "all" frame $i]
> $all move [measure fit $sel $sel_cent]
> $sel delete
> $all delete
> }
> set all [atomselect $mol "all"]
> animate write dcd "oligo_aligned.dcd" beg 0 end [expr $numframes - 2] sel
> $all $mol
> exit
> ------------------------------------------------------------------
>
> It seems to do the work, but the sugar ring is aligned in an inverted
> configuration. See the figure attached herewith. The 4x4 matrix has 1 along
> the principal
> It fits C1 to C5 and C2 to C4, C4 to C2 and C5 to C1. Can someone suggest
> me a workaround to fix this?
>
> Regards,
> Mish
>
>
>
>