VMD-L Mailing List

From: Mamoru Yamanishi (myamanishi3_at_unl.edu)
Date: Wed Dec 07 2005 - 12:28:32 CST

Hello All,

I have couple of problems. Since I am new to VMD, I can not
distinguish the problems are relating to my usage, my environments,
or limitation of VMD.

1) MacOS X version did not show "VOLUME" coloring.

        I tested both 1.8.3 and 1.8.4a22 on MacOS X (10.3.4).

        I calculated sspl.dx and pot.dx on another environment (IA32 Linux)
        and wanted to visualize an electrostatic potential surface on
        MacOS X.

        I loaded both *.dx files and chose "sspl.dx" as "Data Set" and
        "pot.dx" as "Volume" coloring method. However, the solvent
        accessible surface was monochrome. I also adjusted
        parameters under "Trajectory", but it had not changed.

        What I did on MacOS X was the same way to show
        a colored electrosttic potential surface on Linux environment.

        My questions are: Are there any incompatibility of *.dx file between
        MacOS X and IA32 Linux? Do I need to change parameters in MacOS X
        version of VMD?

2) Raster3D output was monochrome.

        I tested only 1.8.4a22 on IA32 Linux.

        I wanted to generate Raster3D output of an electrostatic potential surface.
        I could show colored surface using sspl.dx and pot.dx files.

        I chose "Raster3D" under "Render controls dialog, and "plot.r3d"
        was generated. However, the rendered file was black&white (monochrome).

        I wonder whether "plot.r3d" was generated as monochrome or my render
        command didn't work. The axis was rendered in color, and other type of
        representation, for example "tube", gave what I expected.

        The "render" command in Raster3D was modified to render huge objects.
        Its version is 2.7c.

Please give me any suggestions. 

-- 
Mamoru Yamanishi, Ph.D. <myamanishi3_at_unl.edu>
Research Assistant Professor
Dr. Banerjee's Lab., Biochemistry Department
University of Nebraska-Lincoln