What was new in version 2?

Interactive OpenGL VRML 2.0 Image files Raster3D MolAuto External objects interface

Graphics commands Graphics state parameters Command-line options Relaxed command syntax Reimplementation in C

Interactive OpenGL

The rendering is based on the same graphics objects as the other output formats. The 3D OpenGL image is rotatable and scalable using the mouse, and the current rotation matrix can be output for the user to cut-and-paste into the MolScript input file. This considerably simplifies the process of defining a good view of a molecule, previously a cumbersome iterative process.

When an error in the input file is encountered, the OpenGL output mode does not abort the program. Instead, the graphics objects created so far in the script are rendered, so that the user can correct the input file, and re-read it within the same running MolScript process. This speeds up debugging of input scripts, and also makes it easy to test different modifications to the graphics state parameters.

VRML 2.0

The VRML 2.0 specification supports dynamic behaviour, and features based on this may be included in future versions of MolScript. Currently, investigations are being made to test support for dynamic behaviour in the models, such as molecular dynamics, illustrations of enzymatic reactions, or depiction of changes in quaternary structure.

Image files

Raster3D

• Labels can now be output, provided that the GLUT library has been installed.
• Transparency has now been implemented.
• MolScript now gives a much higher degree of control over the contents in the header section of the Raster3D input file. For example, the size of the image is now determined through the command-line option -size.

MolAuto

The MolAuto program considerably simplifies the process of creating new MolScript images. The behaviour of MolAuto can be controlled to some degree by command-line options.

External objects interface

The appearance of the objects is determined by the same parameters as the ordinary graphical objects in MolScript. It is also possible to specify explicit colours in the object file. The object coordinates may be transformed by the view matrix specified by the most recent transform command.

Graphics commands

• cylinder, a new representation for helices.
• double-helix, a schematic representation for nucleotide chains.
• object, importing graphical objects (lines, points, triangles) from external files.
• anchor, Web links for VRML.
• viewpoint for VRML.
• header commands, for better control of global properties.
  • frame
  • headlight
  • shadows
  • fog
• residue selections:
  • model, for NMR protein structures.
  • ligands
  • amino-acids also select the residue types ASX and GLX.

Graphics state parameters

• colourparts, the basis for residue-by-residue colouring of residue representations.
• bondcross, for displaying non-bonded atoms with the bonds command.
• colourramp, to set the colours of residues and atoms.
• hsbreverseramp
• emissivecolour
• specularcolour
• transparency

Command-line options

• The options -in, -out and -log have been added for better control of input, output and message log files.
• The option -raster3d as a synonym for -r, and -silent for -s, have been added, as more comprehensible synonyms.
• The option -e for the Encapsulated PostScript (EPS) output mode has been removed, and replaced by -eps. This reflects the completely new implementation of this format.

Relaxed command syntax

• Input lines may now be any length. The previous versions had a limit of 80 characters, due to the limitations of standard Fortran 77 i/o.
• A single lexical item (loosely: word or string) may now be up to 2047 characters long.
• The commands in the header such as slab and window may now be given in any order. Previously, there was a strict and not completely logical ordering of these commands.
• Numerical floating-point values (for example: 1.0) may now be given as integers also (now: 1). The decimal point is no longer necessary.
• Double-quotes '"' are not necessary for strings which have no blank characters or special characters. This is useful for file names (coordinate files, object files,...) or identifiers (atom names, residue names, types, etc).
• Macros may now be defined in the places in the input script file specified by the syntax. The previous version contained a bug in this respect.
• A warning is given if the last residue in a residue sequence selection (from... to...) is not found in the coordinate data.

Reimplementation in C

No static memory limits

In version 2, there are no such limits; all memory usage is dynamic, and the size of the application is now limited only by the physical or virtual memory of your computer. This means that there will be no need to recompile the program when the applications increase in size and complexity.

Increased computational efficiency

The memory footprint of the new version 2 is almost always much smaller than in v1.4, since memory is dynamically allocated only when it is actually needed by the program. In v1.4, memory allocation had to be statically determined at compile time, and therefore set to the maximum expected application size. This could pose a problem on certain computer systems.

Organisation of the source code