VMD-L Mailing List

From: Dr. Seth Olsen (seth.olsen_at_gmail.com)
Date: Thu Sep 21 2006 - 21:50:58 CDT

Hi Axel,

Because I've always wanted a horsemince hamburger, I then did the following
to generate the attached pictures:

To make 'Angstrom3.jpg':
1.deleted everything except the green Angstrom cylinder from the script.
2. started VMD, loaded the attached pdb ('Geometry.pdb'), set rep to CPK
with thin bonds
3. ran the script

To make 'Angstrom4.jpg':
1. started VMD
2. ran the script
3. loaded the molecule

As you can see, I got very different results. The way that the camera
resets upon loading the molecule makes me think that the problem is buried
somewhere in how VMD resets the perspective to accomodate what has been
loaded. Specifically, VMD may always draw the cylinder in the same
dimensions regardless of how the view has been scaled to whatever molecule
is currently loaded.

Cheers,

Seth

On 9/22/06, Dr. Seth Olsen <seth.olsen_at_gmail.com> wrote:
>
>
> Hi Axel,
>
> And just to make sure that the horse is well and truly dead, after adding
> an extra line to the script so that after making the black cylinder and then
> loading the pdb, it creates another graphics molecule containing a cylinder
> with the same endpoints (+/- 0.5 on the x axis), colored green with a
> larger radius. The error reappears. See attached picture.
>
> Cheers,
>
> Seth
>
> On 9/22/06, Dr. Seth Olsen <seth.olsen_at_gmail.com> 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.
> > >
> > >
> >
> >
> > --
> > 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.
> >
> >
>
>
> --
> 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.
>
> 

-- 
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.

Angstrom3.jpg Angstrom4.jpg