VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Mon May 24 2004 - 12:44:03 CDT

On Mon, 24 May 2004, B.D Allen wrote:

BA> Hi all,
BA> I've just started ising VMD and have a couple of questions.
BA> Firstly, is it possible to create a mapped isosurface?(preferably
BA> animated during a trajectory) For example, I want to display the
BA> electrostatic potential or spin density mapped onto an electron density
BA> isosurface. I have written scripts to load up multiple gaussian cube
BA> files to display, for example orbitals during a trajectory, but can't
BA> figure out a way to do the mapping. Has anyone ever tried this?

hi,

mapped isosurfaces are not available for vmd 1.8.2. it has been
implemented in the current development version, though.

as for the movie itself. you may want to check out
<http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect6>
if your implementation is significantly different,
i'd like to have a look at it. it may be a nice addition
to my collection of visualization examples.

BA> Secondly, when I try and create a 'VolumeSlice' representation of one of
BA> my cube files, nothing appears on the screen. Is there a special colour
BA> to select? In case it's a bug, I running VMD 1.8.2 on Windows 2000.

are you sure the slice is visible? AFAIK, vmd estimates the initial
scaling factor from the atom coordinates. depending on the size
of your cube, you may see it if you zoom out. also
check out the mailing list archives, this may be a driver issue.

BA> Finally, (and this may be a TCL scoping question) when I trace a
BA> variable (in my case vm_frame) from within a script, it doesn't
BA> recognize the trace from outside of the script (i.e. when the script
BA> returns to the command prompt). I have to trace the variable manually at
BA> the command prompt for the effect to be global. Is there any way around
BA> this?

this is difficult to tell without seeing the code.
you may have to import the variable from the global
namespace with 'global vmd_frame'. i usually add the
traces in the top level, so i never noticed.

hope this helps,
        axel.

BA>
BA> Sorry for the long questions, and thanks in advance
BA>
BA> Ben
BA>
BA>
BA> Ben Allen
BA> Molecular Photonics Laboratory
BA> School of Natural Sciences
BA> Bedson Building
BA> University Of Newcastle Upon Tyne
BA> Newcastle Upon Tyne
BA> NE1 7RU
BA>
BA> +44 (0)191 2226485
BA>
BA> 

-- 
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Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
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