VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Fri Nov 16 2007 - 17:12:27 CST

Dear VMD,

I noticed that when I load a molec (amber parm7 formatted)
into VMD and use
Extensions -> analysis -> rmsd trajectory tool
that I get a different answer when I do the same calculation using
script commands.

After a bit of checking it seems that the

backbone button in the gui selects (name C CA N)
while backbone in the text graphical selection is (name C CA N O )

If I use (name C CA N ) instead of backbone as in the attached script I
get the same answer as gui.

Just my $.00001/2
Tom

**************************************
set thismol [molinfo top]
set all [atomselect top all]
set nf [molinfo top get numframes]
 

set fraglist [lsort -unique [$all get pfrag ] ]
set fraglist [lrange $fraglist 1 [ llength $fraglist ] ]

##
## GEE WOULDN"T IT BE NICE TO HAVE A
## molinfo top numpfrags
### and
## molinfo top numnfrags
## type command
##

foreach frag $fraglist {
 set frame0fragbb [atomselect top "pfrag $frag and name C CA N" frame 0]
  set frame0frag [atomselect top "pfrag $frag " frame 0 ]

  set fragbb [atomselect top "pfrag $frag and name C CA N" ]
  set frag [atomselect top "pfrag $frag " ]

  for { set i 0 } { $i < $nf } { incr i } {
  $fragbb frame $i
  $frag frame $i
  $all move [measure fit $frag $frame0frag ]
  puts "$i [measure rmsd $frame0fragbb $fragbb ] "
  puts "$i [measure rmsd $fragbb $frame0fragbb] [measure rmsd $frag
$frame0frag]"
}

}

quit