[Molvis-list] Re: Advice on rendering superposed pdb files

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Wed Oct 11 16:35:23 EDT 2006

I assume we are talking about good printer renderings, as opposed to
good screen renderings.

The quality of renderings, is, of course a matter of taste,
hardware and journal requirements.  That being said, I personally
find the renderings done by Raster3D to be superb.

When I am in a hurry and need to do as reasonably good rendering
directly from RasMol, I usually go to a computer with a large
monitor, and set up a full-screen display in 32 bit mode and
export a pict, which I then process with the usual graphics
manipulation programs to get a clean print image.

I have been testing code for direct export from RasMol to
Raster3D scripts.  If you would like to test it and suggest
improvements, please contact me.

If you are taking about the pinched waists on the screen renderings,
that is RasMol's flag for alternate conformer bonds.  If you remove
the alternate conformer flags, and use MODEL ENDMDL pairs
instead, the narrowed waists will go away, and you should get
the renderings you are expecting.  You can see a jpeg
from RasMol (via a pict) at:


     H. J. Bernstein

At 5:39 PM +0530 10/11/06, abi_chem at iiit.net wrote:
>Dear Prof. Bernstein,
>We have developed a simple algorithm for superposing pdb files for two
>base pairs and creating the pdb file for the superposed pairs. In the
>superposed pdb file we have provided the two base pairs respectively with
>different temperature factors and different chain ids so that they may be
>viewed in different colors. Unfortunately, the rendering in Rasmol is not
>coming out at all well. The two gif files show the quality of rendering in
>different modes and the .pdb file is the file corresponding to the first
>superposition step.
>Could you please suggest a method for a better rendering using Rasmol or
>any other software?
>Thanking you in advance.
>Dr. Abhijit Mitra
>IIIT Hyderabad
>Hyderabad 500032
>Attachment converted: Macintosh HD:1.GIF (GIFf/«IC») (003DD57F)
>Attachment converted: Macintosh HD:Test1mod.pdb (    /    ) (003DD580)
>Attachment converted: Macintosh HD:superposed.GIF (GIFf/«IC») (003DD581)

  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

               Office:  +1-631-244-3035
            Lab (KSC 020): +1-631-244-3451
                  yaya at dowling.edu

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