VMD-L Mailing List

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Mon Mar 16 2009 - 15:39:26 CDT

Hi,

in the tutorial multiple molecules and scripting,
http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node3.html

there is a method to color a protein based on distance deviation.

lets say i want to output a number for this distance deviation
say i have a pre-minimization structure 1DGC and a post minimization
structure 1DGC

i can load 1DGC as 0 and 1DGCmin as (1), and write

set crystal [atomselect 0 "all"]
set atomsel1 [atomselect 0 "protein and alpha"]
set atomsel2 [atomselect 1 "protein and alpha"]
set M [measure fit $atomsel1 $atomsel2]
$crystal move $M --this is to get a picture of the alignment
and then
set Dev [measure fit $atomsel1 $atomsel2] --but this will give me {1.0
0.0 0.0 0.0} {0.0 1.0 0.0 0.0} {0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}

but, there is actually a slight deviation, it can be seen from the
picture, am i using the wrong command?