From: Cojocaru,Vlad (
Date: Sun Apr 29 2007 - 15:12:54 CDT


Mea culpa for the "foggy" description I gave. But Olaf guessed correctly what i meant.
My goal was to take a picture of some cavities on a protein surface. To do that I turned on depth cueing but I realized that the display (VMD display before taking any picture) even for close objects (protein surface) was very dark. Then I took some test pics with Tachyon and povray but the image was simply to dark to distinguish anything on it. In order to get some light I turned all lights on but with no effect. In fact I only got some light on the nearby objects if I scaled and moved the view inside the protein. But what I wanted was to picture the protein surface, so this was no useful ...

Tomorrow I will test Olaf's solutions.

Thanks for answering both to Alex and Olaf and sorry again for not being clear enough in my first email.



-----Original Message-----
From: Axel Kohlmeyer []
Sent: Sun 4/29/2007 7:43 PM
To: Olaf Lenz
Cc: Cojocaru,Vlad; VMD list
Subject: Re: vmd-l: increase light under depth cueing

On Sun, 29 Apr 2007, Olaf Lenz wrote:

OL> Hash: RIPEMD160
OL> Hello!
OL> Axel Kohlmeyer wrote:
OL> > VC> I was trying to render an image using depth cueing (vmd 1.8.6). However,
OL> > VC> even if I have all lights on, the image remains very dark ...
OL> I think I understand what Vlad means, as the effect actually kept me
OL> from using depth cueing even though it is useful in many cases. The
OL> problem he describes is, that the "fog" starts right at the eye, so that
OL> even the parts closest to the observer can already look cued and faded.

which, if correct, would (again) prove, that the kind of help one
can provide depends very much on asking the right questions and
providing an accurate descriptiong of the problem. 'render' implies
for me using an external renderer and 'display' would imply the default
OL> Quick answer: to make the image less faded, choose the translation mode
OL> (press 't'), press and keep the middle mouse button pressed, and move
OL> the mouse left or right. This will probably do what you want.

in order to add any useful content, i'd also like to draw your attention
to the Display Settings dialog (and the corresponding script commands)
that allow to fine tune the settings for depth cueing, particularly
the cue density.


OL> Longer answer:
OL> The key is to realize that there is a difference between scaling the
OL> molecule and translating the molecule in and out of the screen.
OL> When using the mouse wheel or the scaling mode (press 's'), you "scale"
OL> the molecule. This can be thought of as using a camera and zooming in or
OL> out. As for the depth cueing, the amount of fog between the eye and the
OL> molecule does not change, therefore the image looks still as faded as
OL> before.
OL> To "translate" the molecule, choose translation mode (press 't'), press
OL> the middle mouse button and keep it pressed, and move the mouse left or
OL> right. This will move the camera position in and out. When you are
OL> closer to the molecule, there is less fog, and the colours look less faded.
OL> In fact, this has very much confused me at first, as I'm a fan of the
OL> orthographic projection mode. When cueing is turned off, translating the
OL> molecule in and out the screen has no visible effect at all. Only when
OL> cueing is turned on, the amount of fog is changed, but the size of the
OL> image is still constant. This is something that would be nice for the docs!
OL> Olaf
OL> Version: GnuPG v1.4.2 (GNU/Linux)
OL> Comment: Using GnuPG with SUSE -
OL> iD8DBQFGNFfmtQ3riQ3oo/oRA30iAJ4pVFob/kFW2cK5uWNH31eISm9aTQCghM22
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Axel Kohlmeyer
   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.