VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 07 2011 - 18:11:44 CDT

On Wed, Sep 7, 2011 at 7:02 PM, winardi, erik <egw24_at_yahoo.com> wrote:
> Dear Dr. Kohlmeyer,
> I was mistaken on giving the information.
> What I have is the .dcd format not .pdb which is also a trajectory file
> only.
> I could upload the .dcd file but I can only draw the bonds in VMD using
> dynamic bonds.
> But I couldn't draw the atoms using VDW or CPK. Is there anyway I can
> visualize the atoms ?

yes. the problem is, that a dcd file has no information
about the atoms, so all of those fields are left empty,
i.e. their radius is listed with 0.0 (thus no VDW or CPK),
their element is empty (hence no heuristic bond search).

> or I need to get the .pdb or .car file ?

you can just run the following script code:

set sel [atomselect top all]
$sel set radius 1.5
$sel set name A

that should make VDW work again, but
doesn't identify atoms by element.

having a .pdb or something else with
element information would help.

if you have only mass information,
you could use:

topo guessatom element mass
topo guessatom name element
topo guessatom radius element
mol bondsrecalc top

to recover information with some heuristics.

http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-guessatom-property-from-

cheers,
    axel.

>
> Thanks,
> Erik
> ________________________________
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: "winardi, erik" <egw24_at_yahoo.com>
> Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Sent: Wednesday, September 7, 2011 2:55 PM
> Subject: Re: vmd-l: Visualizing Trajectory file: .pdb or .xyz
>
> On Wed, Sep 7, 2011 at 2:49 PM, winardi, erik <egw24_at_yahoo.com> wrote:
>> Dear VMD community,
>> I have trajectory files which need to be visualize. They are in .pdb and
>> .xyz format.
>> I do not have the initial configuration data for these trajectory files.
>> I tried loading these trajectory files into VMD and playing around the
>> Graphic Representation Tools.
>> However, I couldn't get the atoms to appear. I chose the VDW molecule
>> type.
>> Is it possible to visualize the atoms and bonds only from .pdb or .xyz
>> files
>> ?
>> or do I need to get the initial configuration too ?
>
> no. both file formats, .xyz and. pdb, contain coordinate information.
>
> please have a close look at the VMD console
> and check if there are any error messages.
>
> VMD will do a best effort to parse files according
> to the available "standards" and some commonly
> used variants, but if the format strays too far, the
> corresponding plugin may reject reading the files.
>
> if there is no message visible, please provide small
> example files demonstrating the issue.
>
> cheers,
>     axel.
>
>> Thanks,
>> Erik Winardi
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.