VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 30 2012 - 12:49:51 CDT

On Fri, Mar 30, 2012 at 12:37 PM, james Fernandez
<fernandezjames89_at_gmail.com> wrote:
> Hi VMD USERS,
>         I am trying to plot some co-ordinates(points) on VMD and I used a
> simple format of a PDB file but its giving a wrong figure.
> The format of the pdb file that i used is as follows,
>
> 8!
> REMARK 350 BIOMOLECULE: 1
>
> ATOM      1       28.407  28.897   5.314  1.00  9.00
> ATOM      2       28.238  28.590   4.518  1.00  9.00
> ATOM      3       28.343  27.156   2.578  1.00  9.00
> ATOM      4       24.707  24.752   0.377  1.00  9.00
> ATOM      5       24.641  22.884   -1.74  1.00  9.00
> ATOM      6       23.405  19.850   -3.63  1.00  9.00
> ATOM      7       22.710  16.487   -4.12  1.00  9.00
> ATOM      8       22.205  13.628   -5.88  1.00  9.00
>
> I am trying to connect these molecules through bonds i am able to connect it
> but the co-ordinates that are getting plotted on VMD are not accurate.
>
> Can someone please help me in getting these co-ordinates plotted since I am
> NEW to this software. I will be very thankful to you and your help will be
> appreciated.

your "pdb" format does not conform with the
requirements of the pdb standard. no surprise
that VMD will give you crap. you have to write
your files according to the corresponding format
standards.

this has *nothing* to do with VMD, by the way.

axel.

>
> Regards
> James 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.