VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 27 2018 - 10:12:23 CST

Hi,
  Yes, it should be noted that the existing implementations of the
"measure fit" routines in VMD are not symmetry-aware, so things like
rings could be a potential problem. As you have discovered, one can
work around this by changing the atom indexing order to accomodate
the symmetry, etc.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 27, 2018 at 03:25:29PM +0000, mish wrote:
> Hi again,
> I fond the issue. It was possible to assign the order {...}Â and then it
> works fine!
> Best,
> Mish
> On Tue, Nov 27, 2018 at 2:58 PM mish <[1]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[2].nc" parm7 "oligo.parm7"]
> set numframes [molinfo $mol get numframes]
> for { set i 0 } { $i < $numframes } { incr i } {
> Â set sel [atomselect $mol "resid 4 and name C1 C2 C3 C4 C5 O5" frame
> $i]
> Â set all [atomselect $mol "all" frame $i]
> Â $all move [measure fit $sel $sel_cent]
> Â $sel delete
> Â $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 principalÂ
> Â 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
>
> References
>
> Visible links
> 1. mailto:smncbr_at_gmail.com
> 2. http://dehydr.nc/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/