VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Nov 17 2007 - 00:11:54 CST

On Fri, 16 Nov 2007, Thomas C. Bishop wrote:

TB> Dear VMD,

tom,

can you please state which version of VMD and
the RMSDTT plugin you are using.

in the version of rmsdtt, that ships with the
current version of VMD (rmsdtt 2.0) you can
change the definition of what represents the
backbone in its options menu (Options->Backbone Def).
it defaults to "C CA N", but you can change this
to "C CA N O" which in turn would be consistent
with the backbone keyword of VMD's atomselect command.

it would be more consistent with the rest of VMD
to change the default, but i guess this is also
a matter of taste and ultimately the choice of
the author of the plugin.

cheers,
  axel.

TB> I noticed that when I load a molec (amber parm7 formatted)
TB> into VMD and use
TB> Extensions -> analysis -> rmsd trajectory tool
TB> that I get a different answer when I do the same calculation using
TB> script commands.
TB>
TB> After a bit of checking it seems that the
TB>
TB> backbone button in the gui selects (name C CA N)
TB> while backbone in the text graphical selection is (name C CA N O )

TB>
TB> If I use (name C CA N ) instead of backbone as in the attached script I
TB> get the same answer as gui.
TB>
TB> Just my $.00001/2
TB> Tom
TB>
TB>
TB> **************************************
TB> set thismol [molinfo top]
TB> set all [atomselect top all]
TB> set nf [molinfo top get numframes]
TB>
TB>
TB> set fraglist [lsort -unique [$all get pfrag ] ]
TB> set fraglist [lrange $fraglist 1 [ llength $fraglist ] ]
TB>
TB> ##
TB> ## GEE WOULDN"T IT BE NICE TO HAVE A
TB> ## molinfo top numpfrags
TB> ### and
TB> ## molinfo top numnfrags
TB> ## type command
TB> ##
TB>
TB> foreach frag $fraglist {
TB> set frame0fragbb [atomselect top "pfrag $frag and name C CA N" frame 0]
TB> set frame0frag [atomselect top "pfrag $frag " frame 0 ]
TB>
TB> set fragbb [atomselect top "pfrag $frag and name C CA N" ]
TB> set frag [atomselect top "pfrag $frag " ]
TB>
TB> for { set i 0 } { $i < $nf } { incr i } {
TB> $fragbb frame $i
TB> $frag frame $i
TB> $all move [measure fit $frag $frame0frag ]
TB> puts "$i [measure rmsd $frame0fragbb $fragbb ] "
TB> puts "$i [measure rmsd $fragbb $frame0fragbb] [measure rmsd $frag
TB> $frame0frag]"
TB> }
TB>
TB> }
TB>
TB> quit
TB> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.