VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 05 2016 - 02:30:05 CST

You need to have a "molecule" created 1st. Usually one would have a PDB or such of the structure and load the electron density on top of it, to visualize. If you don’t have a PDB or any other structure file, do just in console:

mol new

This will create an empty molecule, which should allow adding the volume data to it, and visualize it.

Norman Geist

> -----Ursprüngliche Nachricht-----
> Von: Irem Altan [mailto:irem.altan_at_duke.edu]
> Gesendet: Donnerstag, 4. Februar 2016 15:30
> An: Norman Geist <norman.geist_at_uni-greifswald.de>
> Betreff: Re: vmd-l: loading electron density maps with a script
>
> Hi,
>
> Thank you for your answer. I guess I don’t know how to activate a
> representation. Do I need to go through and extra step to make it appear on
> the “selected molecule” list in the graphical representations window?
>
> Best,
> Irem
>
> > On Feb 4, 2016, at 2:33 AM, Norman Geist <norman.geist_at_uni-
> greifswald.de> wrote:
> >
> > Hi Irem,
> >
> > I guess you will have to activate an representation with a "drawing
> method" able to "show" volume data. The most suitable for electron density
> data might be "Isosurface" where you need to select the "Vol" dataset 1st,
> and then play with the "Isovalue". You might need multiple representation
> with different "Isovalue" to fit your needs.
> >
> > Let us know & good luck
> >
> > Norman Geist
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Irem Altan
> >> Gesendet: Mittwoch, 3. Februar 2016 23:03
> >> An: vmd-l_at_ks.uiuc.edu
> >> Betreff: vmd-l: loading electron density maps with a script
> >>
> >> Hi,
> >>
> >> I want to load electron density maps using a tcl script. I have found the
> >> following script that just does that:
> >>
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readedm/read
> >> edm.tcl
> >>
> >> However, at the end of the scripts it says as a comment that “VMD now
> has
> >> the data, and its up to the user to activate representations on it.” I am not
> >> sure what is meant by this. How can I make the map appear in the
> OpenGL
> >> display? (It does not show up on the list of representations)
> >>
> >> Best,
> >> Irem
> >