From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Apr 02 2009 - 11:46:33 CDT

On Thu, 2009-04-02 at 16:58 +0200, Kalavera_at_gmx.net wrote:
> Problem solved:
> After watching my PDB-file in detail again there came up an unusually entry in every row, e.g.:
>
> ATOM 43808 CLA CLA 33 24.508 4.158 -53.556 1.00 0.00 ION CL
>
> The last entry "CL" caused the trouble. If I use this line :
>
> ATOM 43808 CLA CLA 33 24.508 4.158 -53.556 1.00 0.00 ION

actually, the last entry is required by the PDB standard
(specifies the element). but it us exactly what made VMD
choose the different size. if you remove the line, VMD will
assume CLA to be a carbon and use the size of a carbon.

cheers,
   axel.

> the ions are both the same size.
> Thx for the support, Axel
>
> your M.Kalavera
>
>
> -------- Original-Nachricht --------
> > Datum: Thu, 02 Apr 2009 10:25:33 -0400
> > Von: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> > An: Kalavera_at_gmx.net
> > CC: vmd-l_at_ks.uiuc.edu
> > Betreff: Re: vmd-l: Problem with autoionize ?
>
> > On Thu, 2009-04-02 at 15:50 +0200, Kalavera_at_gmx.net wrote:
> > > hello everybody,
> > > after using the autoionize script from Ilya Balabin and Marcos Sotomayor
> > > (http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/)and exchanging
> > the sodium with potassium I got confused by the visual results in VMD,
> > because of different radii for potassium and chloride ions.
> > > In my case the chloride ion is displayed nearly two times smaller than
> > the potassium if VDW is used as the drawing method. I need to know if this
> > is the normal case and whether my system is setup properly.
> >
> > unless you use a file format that contains explicit radii,
> > VDW uses covalent radii from an internal table. those have
> > no idea that you have ions. in general, you have to keep in
> > mind that VMD knows only what is provided. it deliberately
> > does not know any chemistry.
> >
> > cheers,
> > axel.
> >
> > > Thx for your replies,
> > > M.Kalavera
> >
> > --
> > =======================================================================
> > 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.

-- 
=======================================================================
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.