VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jul 23 2008 - 06:36:25 CDT

On Wed, 23 Jul 2008, Ignacio Fernández Galván wrote:

IFG> --- On Tue, 22/7/08, Eduardo Cruz-Chu <chucruz_at_ks.uiuc.edu> wrote:
IFG>
IFG> > you can use equations in your selection. For instance, to
IFG> > select a cylindrical region of radius R around a point
IFG> > (Xcenter,Ycenter) in the frame F
IFG> >
IFG> > set sel [ atomselect top "(x-$Xcenter)*(x-$Xcenter) +
IFG> > (y-$Ycenter)*(y-$Ycenter) < $R*$R" frame $F ]
IFG> >
IFG> > you can limit the region of the cylinder adding extra
IFG> > equations in the Z direction.
IFG>
IFG> Yes, that's what I tried as the "hard way", but somehow the variables are not evaluated inside the selection. The problem may be that I'm writing the selection formula in the GUI for representations (or in the "mol selection" line in a state file previously saved). So:
IFG>
IFG> set xA 2
IFG> ...
IFG> mol selection {x < $xA}
IFG> ...
IFG> mol addrep top
IFG>
IFG> but the selection comes out as if I had written "x < 0" instead of "x < 2". Of course, if I write "x < 2" directly, it works as it should, so at the end I could "hard code" the values in the state file, but I'd prefer to avoid that.

yes. this cannot work. the selection parser does not have
access to any tcl variables as it operates on a lower level.

if you don't want to use the dummy atom option that i suggested,
and compute everything explicitly, you can use the "user" field
to store per-timestep information about each atom of your system.
this can not only be used to color code atoms but to do selections
(user > 0).

cheers,
   axel.

IFG>
IFG> > If your benzene ring is moving, you should play with the
IFG> > equations (find the center of the ring, can use the middle
IFG> > point between 2 carbons, and the normal to the ring plane,
IFG> > can use three carbons).
IFG>

IFG> Ok, in my case it is actually not moving, because I'm centering it
IFG> at every frame. But if it were, how would I do it so that the
IFG> selection would be updated at each frame? For doing analysis and
IFG> calculations, I can use a foreach loop and get the coordinates each
IFG> frame, but what can be done for a representation? The "update
IFG> selection every frame" is not enough, because I'd need a way to
IFG> define the xA variable every frame...
IFG>
IFG>
IFG>
IFG>
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IFG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.