VMD-L Mailing List

From: mish (smncbr_at_gmail.com)
Date: Tue Nov 27 2018 - 08:58:09 CST

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