From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Thu Oct 27 2005 - 12:57:46 CDT

Hi there, I'm trying to cut a PBC box out of a cube of waters
surrounding a molecule. I'm using the Gramicidin A example
(http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/).

I've carefully arranged my molecule to the origin of the large water
box. I'm now trying to chop off all the waters outside this
(octahedral box) with the tcl commands

set sel [atomselect top \
      "water and same residue as (not hydrogen and (x < -14.99 or x >
14.99))"]
      $sel set beta 1
      $all move [transaxis z 120]
}

I have previously defined "all" in the usual way.

I expect this to rotate on the z-axis, leaving a octahedral box,
essentially centered on my molecule. What I get is unexpected --- it
seems that the rotation axis has been shifted off the z-axis. Here
is a picture of the result (small 60k image), showing the *removed*
waters:


I have lined up the VMD axes at the origin. Why isn't it centered
where I expect?

Cheers,

Mike

--
C. Michael McCallum           http://chemistry.cop.uop.edu/ 
cmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax