VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 20 2010 - 13:04:57 CDT
- Next message: John Stone: "Re: Cannot find "cionize plugin" in VMD"
- Previous message: John Stone: "Re: Cannot find "cionize plugin" in VMD"
- In reply to: Thomas C. Bishop: "trajectory sort by RMSD or other"
- Next in thread: Thomas C. Bishop: "Re: trajectory sort by RMSD or other"
- Reply: Thomas C. Bishop: "Re: trajectory sort by RMSD or other"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
tom,
On Tue, Jul 20, 2010 at 1:17 PM, Thomas C. Bishop <bishop_at_tulane.edu> wrote:
> Does anyone have a tool handy that allows you to arbitrarily reorganize the
> animation display order of a DCD file.
no. you'd have to swap coordinates around if you want to use
the standard animation control dialog.
> For example play a trajectory in the order of increasing RMSD instead of the
> actual time order.
>
> This can be accomplished with a list of frame numbers and an "animate goto"
> coupled with a trace variable in tcl.
> In general the list of frame numbers can come from anywhere.
this would not work, since the animate goto would trigger
the reorder event and you'd have a deadlock.
the best you can do is something like the following (untested):
set mol [molinfo top]
set nf [molinfo $mol get numframes]
set sel [atomselect $mol all]
set refsel [atomselect $mol all frame 0]
set rmsdlist {}
for {set i 0} {$i < $nf} {incr i} {
$sel frame $i
lappend rmsdlist [list $i [measure rmsd $sel $refsel]]
}
set gotolist [lsort -increasing -real -index 1 $rmsdlist]
for {set j 0} {$j < 10} {incr j} {
for {set i 0} {$i < $nf} {incr i} {
animate goto [lindex $gotolist $i 0]
display update
display update ui
after 100
}
}
if you want something more fancy with a GUI,
you could rip off the multimonanim plugin for it.
cheers,
axel.
> The problem however is what should the trace variable be... I guess it can't
> be the frame number.
>
>
> Any tips or suggestions much appreciated.
> Thanks in advance,
> TOm
>
> *******************************
> Thomas C. Bishop
> Tel: 504-862-3370
> Fax: 504-862-8392
> http://dna.ccs.tulane.edu
> ********************************
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
- Next message: John Stone: "Re: Cannot find "cionize plugin" in VMD"
- Previous message: John Stone: "Re: Cannot find "cionize plugin" in VMD"
- In reply to: Thomas C. Bishop: "trajectory sort by RMSD or other"
- Next in thread: Thomas C. Bishop: "Re: trajectory sort by RMSD or other"
- Reply: Thomas C. Bishop: "Re: trajectory sort by RMSD or other"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]