VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Mon Nov 19 2007 - 10:27:02 CST

I'm using VMD 1.8.5 w/ RMSDTT v2.01
and now that you point it out I see the
Options->Backbone Def.

Thanks for the info.

Note also that my script changes the coords and
that for it to really work correctly (calculate the rms for two
different fittings) then it needs two
move statements (one for each RMSD calc) rather than the one move
statement that's currently included. something similar to following
should work

$all move [measure fit $fragbb $frame0fragbb ]
set bbrms [measure rmsd $fragbb $frame0fragbb ]

$all move [measure fit $frag $frame0frag ]
set allrms [measure rmsd $frag $frame0frag ]

puts "$i $bbrms $allrms "

TOm
 

On Sat, 2007-11-17 at 11:41 +0530, Axel Kohlmeyer wrote:
> 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>
> 

-- 
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*  Thomas C. Bishop   *
*Office: 504-862-3370 *
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