VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Sun Sep 19 2010 - 20:55:47 CDT

> or by loading a file format that includes explicit bond information.

Yes,This works well !

> You can fix this by setting the atomic element types and/or atom radii
> manually,

After change the radius value, how to let display take effect immediately ？
I try "display update", but nothing happens within the display window.

Cheers,

Cun Zhang

On Mon, Sep 20, 2010 at 8:46 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> This is because you're using an XYZ file, and the waters are so
> close together that VMD thinks they are bonded. This is also related
> to the choice of atom names, as VMD guesses atom radii and other
> properties from atom names, but only if they are specified using the
> Protein Databank (PDB) conventions. Otherwise it uses some simpler
> guesses, and in your case it is guessing wrong. You can fix this by
> setting the atomic element types and/or atom radii manually, or by
> loading a file format that includes explicit bond information.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 17, 2010 at 03:37:03PM +0800, Cun Zhang wrote:
> > hi, John
> > I find vmd can't display water molecules rightly in some case( vmd
> > 1.8.8a7).
> > Some molecues are regarded as one molecule. It's so weird.
> >
> > Thank you!
> >
> > Cun Zhang
> >
> > The following is th testing file. And a screenshot is attached.
> >
> > cunzhang_at_Debian:$ cat test.xyz
> > 12
> > generated by VMD
> > OW 140.621994 122.303001 119.871002
> > HW 140.358002 121.397003 119.541000
> > HW 140.434998 122.984001 119.163002
> > OW 143.095993 122.399002 121.165001
> > HW 142.190002 122.556000 120.774002
> > HW 143.725006 123.107002 120.845001
> > OW 142.955002 119.873001 120.723999
> > HW 143.567001 119.393997 121.352997
> > HW 143.102005 120.859001 120.802002
> > OW 140.755005 119.730003 119.224998
> > HW 141.153000 120.091003 118.382004
> > HW 141.460007 119.676003 119.931000
> >
> > --
> > Blog: http://www.edwardpku.com/cun
>
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Blog: http://www.edwardpku.com/cun