From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Wed May 13 2009 - 22:25:22 CDT

Hi all VMD users!

 

I want to move protein atoms of each strcuture from a dcd file to a position where alpha carbon of first residue will be located at point {0 0 0}. I tried the script:

 

set O [atomselect top "protein and resid 1 and alpha"]

set nf [molinfo top get numframes]

set protein [atomselect top "protein"]

set indices 0;

set newcoords 0;

lvarpop newcoords

set indices [$protein get index]

for {set i 0 } {$i < $nf } { incr i } {

$O frame $i

$protein frame $i

set A [lindex [$O get {x y z}] 0]

for {set j 0 } {$j < 882 } { incr j } {

set sel [atomselect top "index $j" frame $i]

set coor [lindex [$sel get {x y z}] 0]

set r [vecsub $coor $A]

lappend newcoords $r

}

$protein set {x y z} $newcoords

}

 

 

 So it apperas the following mistake: vecsub: two vectors don't have the same size

 

I wait somebody can help me.

 

 

Thanks a lot

 

Andres

 

 

 

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