VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 21 2006 - 21:37:27 CDT

Hi Seth,
please try resetting the view after drawing graphics by pressing the =
key; this will ensure that everything is scaled identically.
Best,
Peter

Dr. Seth Olsen wrote:
> Hi Axel,
>
> To be more specific about that last statement, if you change the script so
> that it loads the PDB after creating and drawing the graphics molecule,
> then
> things seem to work (in the sense that the graphics are not distorted. In
> case it might be of use, I'm attaching my .vmdrc file this time.
>
> Cheers,
>
> Seth
>
> On 9/22/06, Dr. Seth Olsen <seth.olsen_at_gmail.com> wrote:
>>
>>
>> Hi Axel,
>>
>> If this is the case, then something is definitely wrong. Attached please
>> find a python script named 'VMDAngstrom.py', a pdb file named '
>> AngstromScale.pdb', and a JPG file named 'Angstrom.jpg'. The pdb
>> contains
>> 2 nitrogen atoms placed at (- 0.5,0.0,0.0) and (0.5,0.0,0.0). The script
>> loads this pdb (lines drawstyle), then creates a graphics molecule and
>> draws
>> a thick black cylinder cylinder with endpoints at (-0.5,0.0,0.0) and
>> (0.5,
>> 0.0,0.0). The JPG shows just what I got when I ran the script.
>>
>> I am running a precompiled linux binary of VMD 1.8.5. I have pointed
>> PYTHONHOME to a precompiled python binary (compiled for 1.8.4, but there
>> is no current distribution as far as I can tell). My OS is FC5
>> running on a
>> P4.
>>
>> What's even more frustrating is that it seems that different results are
>> obtained if you create the graphics molecule, then load the pdb.
>> Regardless, I don't think this is the way VMD was intended to work.
>>
>> Cheers,
>>
>> Seth
>>
>> On 9/22/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>> >
>> > On 9/21/06, Dr. Seth Olsen <seth.olsen_at_gmail.com> wrote:
>> > >
>> > > Hi VMDers,
>> > >
>> > > I've been writing python scripts to visualize 3N dimensional
>> vectors (
>> > i.e .
>> > > molecular modes) as arrows attached to atoms. I've been having a lot
>> > of
>> > > problems with length distortions and after checking my code over
>> > several
>> > > times I think that the problem might be that I have assumed that VMD
>> > uses an
>> > > internal length scale that I am not. What are the units that VMD
>> > uses?
>> >
>> > all graphics objects are drawn on an angstrom scale.
>> >
>> > axel.
>> > >
>> > > Cheers,
>> > >
>> > > Seth
>> > >
>> > > --
>> > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>> > >
>> > > Dr Seth Olsen, PhD
>> > > Postdoctoral Fellow, Biomolecular Modeling Group
>> > > Centre for Computational Molecular Science
>> > > Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
>> > > The University of Queensland
>> > > Qld 4072, Brisbane, Australia
>> > >
>> > > tel (617) 3346 3976
>> > > fax (617) 33654623
>> > > email: s.olsen1_at_uq.edu.au
>> > > Web: www.ccms.uq.edu.au
>> > >
>> > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>> > > The opinions expressed here are my own and do not reflect the
>> > positions of
>> > > the University of Queensland.
>> >
>> >
>> > --
>> > =======================================================================
>> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
>> http://www.cmm.upenn.edu
>> > Center for Molecular Modeling -- University of Pennsylvania
>> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>> > =======================================================================
>> > If you make something idiot-proof, the universe creates a better idiot.
>> >
>>
>>
>>
>> --
>> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>>
>> Dr Seth Olsen, PhD
>> Postdoctoral Fellow, Biomolecular Modeling Group
>> Centre for Computational Molecular Science
>> Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
>> The University of Queensland
>> Qld 4072, Brisbane, Australia
>>
>> tel (617) 3346 3976
>> fax (617) 33654623
>> email: s.olsen1_at_uq.edu.au
>> Web: www.ccms.uq.edu.au
>>
>> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>> The opinions expressed here are my own and do not reflect the
>> positions of
>> the University of Queensland.
>>
>>
>
>