VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Sun Sep 19 2010 - 21:16:00 CDT

It can't work too (command as following). And I will use pdb file as
initial file as your suggestion.
Thank you!

vmd > molecule load xyz test.xyz
vmd > set sel [atomselect top "all"]
atomselect0
vmd > $sel get radius
1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5
vmd > $sel set radius 1.3
vmd > molecule reanalyze top
Info) Analyzing structure ...
Info) Atoms: 12
Info) Bonds: 11
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 0 Nucleic: 0
vmd >

On Mon, Sep 20, 2010 at 9:58 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

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