From: Stephanie Held (
Date: Mon Sep 28 2009 - 08:39:27 CDT


I have a problem concerning vectors in vmd. What I'm trying to do is draw a
cylinder using vmd console which works nicely when I do it like this:

graphics top cylinder {-12.3400001526 73.4120025635 46.4959983826}
{-6.99599981308 63.8670005798 67.9349975586} radius 0.5 resolution 60 filled

Since I have to draw many cylinders I would like to give the positions as
variables instead of numbers in the command:

set a1 [atomselect 0 "resid 33 and type CA"]
set x1 [$a1 get {x y z}]

I did the same for x2 and then tried to draw the cylinder by typing:

graphics top cylinder {$x1} {$x2} radius 0.5 resolution 60 filled yes

But that doesn't work. vmd tells me "need three numbers for a vector" which
doesn't make sense to me because x1 and x2 are actually vectors of three
numbers which I checked:

puts $x1
{-12.3400001526 73.4120025635 46.4959983826}

Does anyone know what to do about this? I'd be very happy about any advice!

Best regards