VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Sep 22 2006 - 18:29:23 CDT

On Fri, 22 Sep 2006, Dr. Seth Olsen wrote:

SO> Hi Axel,

seth,

sorry to be so brief. i'll look into your (many) mails later.
but i have three remarks.

1.) there is a precompiled FC5 rpm for 32-bit linux in the
unofficial/unsupported section of the VMD download area
and on biocore

2.) you do not need a separate molecule for the graphics.
you can add graphics to the id of the loaded molecule.

3.) to make graphics elements vanish, you can either delete
them or create an 'Invisible' material (with 100% transparency)
and change the material. VMD currently only allows one
material per set of graphics for each molecule id, so this
would apply to all graphics elements.

more later, gotta run,
   axel.

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

-- 
=======================================================================
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.