VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Sep 19 2010 - 20:58:44 CDT

Hi,
  After changing the radius, you would probably want to create new
representations, and then delete the old ones, or do a "mol reanalyze"
or something like that. If you set the radii immediately when you load
the file, that will help avoid that problem. Loading your data from files
with explicit bond information is best of course.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 20, 2010 at 09:55:47AM +0800, Cun Zhang wrote:
> A
>
> or by loading a file format that includes explicit bond information.
>
> A
> Yes,This works well !
> A
>
> 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 1/4*
> 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,
> A This is because you're using an XYZ file, and the waters are so
> close together that VMD thinks they are bonded. A 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. A Otherwise it uses some simpler
> guesses, and in your case it is guessing wrong. A 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,
> A John Stone
> A vmd_at_ks.uiuc.edu
> On Fri, Sep 17, 2010 at 03:37:03PM +0800, Cun Zhang wrote:
> > A A hi, John
> > A A I find vmd can't display water molecules rightly in some case(
> vmd
> > A A 1.8.8a7).
> > A A Some molecues are regarded as one molecule. It's so weird.
> >
> > A A Thank you!
> >
> > A A Cun Zhang
> >
> > A A The following is th testing file. And a screenshot is attached.
> >
> > A A cunzhang_at_Debian:$ cat test.xyz
> > A A 12
> > A A generated by VMD
> > A A A OW A A A 140.621994 A A A 122.303001 A A A 119.871002
> > A A A HW A A A 140.358002 A A A 121.397003 A A A 119.541000
> > A A A HW A A A 140.434998 A A A 122.984001 A A A 119.163002
> > A A A OW A A A 143.095993 A A A 122.399002 A A A 121.165001
> > A A A HW A A A 142.190002 A A A 122.556000 A A A 120.774002
> > A A A HW A A A 143.725006 A A A 123.107002 A A A 120.845001
> > A A A OW A A A 142.955002 A A A 119.873001 A A A 120.723999
> > A A A HW A A A 143.567001 A A A 119.393997 A A A 121.352997
> > A A A HW A A A 143.102005 A A A 120.859001 A A A 120.802002
> > A A A OW A A A 140.755005 A A A 119.730003 A A A 119.224998
> > A A A HW A A A 141.153000 A A A 120.091003 A A A 118.382004
> > A A A HW A A A 141.460007 A A A 119.676003 A A A 119.931000
> >
> > A A --
> > A A 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 A A A A A A A A Phone: 217-244-3349
> A WWW: http://www.ks.uiuc.edu/~johns/ A A A Fax: 217-244-6078
>
> --
> 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/      Fax: 217-244-6078