VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Mar 14 2018 - 15:51:06 CDT

Hi Peter,

If I understand this correctly, you start from one molecule loaded with a single frame, apply a single transformation matrix n times, and end up with n+1 total frames written out to some file. If so, you just need to call "animate dup" at the appropriate time, making your script look like this:

set sel [atomselect top all]
set matrix {<4 * 4 transformation matrix>}
set n {10}

for {set i 1} {$i <= $n} {incr i} {
 animate dup frame [expr {$i-1}] top
$sel frame $i
 $sel move $matrix
}
animate write pdb $i.pdb
$sel delete

The other (slower) alternative is to load your initial pdb multiple times until you have as many frames as you need, and then apply your transformation successively.

-Josh

On 03/14/2018 02:43 PM, Peter Mawanga wrote:
Dear VMD users

I am trying to apply a transformation matrix successively to a set of pdb coordinates and save the coordinates after each transformation into a single pdb file. I have been able to write the coordinates separately to multiple files though. My code (attempt) is given below:

set sel [atomselect top all]
set matrix {<4 * 4 transformation matrix>}
set n {10}

for {set i 0} {$i < $n} {incr i} {
 animate write pdb $i.pdb
 $sel move $matrix
 $sel update
}

$sel delete

The "beg <first frame> end <last frame>" could not be applied in this case, since only one frame is involved. Kindly let me know your suggestions. 

--
Cheers
Peter