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How to use your GRASP surface files in Pov4Grasp
How to build a GRASP molecular surface of "good quality"
* How to properly combine GRASP surface files and non-surface objects

How to use your GRASP surface files in Pov4Grasp

It's quite simple !

In this tutorial I will describe the main useful features of this patch version of POV-Ray from the most simple case to some more "complicated" effects that you can achieve. The GRASP surface file that is used here has been built from the X-ray structure of the small Crambin protein. Three different surface properties were calculated and written in the file : electrostatic potentials, surface curvatures, and discrete colors enhancing several residues.

The GRASP file has been written without any transformation or rotations. As the crambin structure coordinates are not centered at the origin, the surface is not centered by default, so we apply a simple translation within the script. Actually this translation uses a macro that allows to keep exactly the same orientation due to the perspective. This macro is called correct_translate in the different exemples, and is defined in the common scene file scene.inc. The latter is an include file which also defines a few global variables. Among them you will find the SYSTEM variable which specify the coordinates system that we use. The following scale <1,1,-SYSTEM> command in the examples insure that the GRASP surface file will always be in the correct coordinates system (GRASP uses a right-handed system while both systems can be used within POV-Ray). Anyway all these stuffs are not really complicated and most of the things are explained in the scene file.

Part 1: Getting started
  1. Our first trial
  2. Let's add some finishes
  3. Adding (multi-layered) textures

Part 2: Surface properties
  1. Mapping a surface property
  2. Changing the property range
  3. Setting the surface transparency
  4. Correcting projected shadows
  5. Adjusting the property colors

Part 3: Discrete colors
  1. Discrete colors on the surface
  2. Setting a global transparency
  3. Reading a color description file

Part 4: Template surfaces
  1. Object copying
  2. The power of template surfaces

How to build a GRASP molecular surface of "good quality"

This tutorial will actually adress several issues on how to get better pictures of your GRASP surfaces. The idea is to produce molecular surfaces with a lot of triangles in order to get smoother shapes, better colors and textures, and to reduce the possible artifacts (incorrectly assimilated to "holes") produced when projecting shadows on it.

Good quality surfaces
  1. What is "good quality" for a GRASP molecular surface ?
  2. Is GRASP able to produce such huge surfaces ?
  3. Which parameter mostly affects the number of triangles ?

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