What is new in v2.1?

New features in v2.1

Backwards compatibility issues

There are a few cases where v2.1 is incompatible with previous versions, and where input files which work for v1.4 (and older) are no longer valid.

Allowed commands within anchor command

The anchor command now allows a more restricted set of commands within the curly brackets, compared to what was allowed in v2.0. This is due to a cleanup of the syntax description, which was sloppy in v2.0. This should not present a problem in most cases, since the commands that have been excluded were unlikely to be used within the anchor command anyway.

Completely different Encapsulate PostScript (EPS) output

The EPS format of the previous versions (v1.4 and older) was fundamentally problematic. It was nearly identical in form with the proper PostScript output. Although formally valid according to the PostScript Reference Manual, it apparently did not satisfy almost any available software.

The new EPS output mode has therefore been completely redesigned to produce a pixel-based image file format, containing a pixmap of the image rendered via OpenGL.

Only PDB coordinate files supported

In the current version, only PDB coordinate files are supported.

The reason for this was that no examples of the other input file formats could be easily obtained for testing during the reimplementation of MolScript.

The other coordinate file formats supported in the previous versions (v1.4 and older) have become even less important since 1993, and the PDB format (with all its limitations and problems) is the undisputed de facto interchange standard for biomacromolecules.

Parameter colourdepthcue removed

The colourdepthcue parameter in the graphics state has been removed. Its functionality has been replaced in version 2 by the fog header command.

The reasons for this change were partly that the function of the old parameter was badly designed, partly that it was difficult to implement it in output modes other than PostScript.

The output mode cannot be specified in the input file

In previous versions of MolScript (v1.4 and older) it was possible to specify the output format produced by MolScript directly in the input file, by giving a keyword encapsulated or raster3d before the first plot. This possibility has been removed. The output format must now be specified as a command-line option.

The reason for removing this feature was that it was messy (both for the user and for the developer of MolScript) to have two different ways of specifying output format. Also, it was unclear how to resolve conflicts between an explicit setting in the input file and a given command-line option.

Crosses will be drawn for non-bonded atoms

A new parameter bondcross was introduced in version 2, which controls the size of crosses drawn for non-bonded atoms in the bonds command. The same behaviour as in previous versions of MolScript (v1.4 and older) can be obtained by setting the value of this parameter to 0.0.

Changes from previous versions

Version history

Version development policy

The development of MolScript progresses at a very uneven speed. New versions containing novel features and/or bug fixes are planned, but the implementation of these take place whenever there is time. No commitment as to release dates can be given.

However, the author gives the following statement of intent:

No new features will conflict with previously available features. Later versions of MolScript will be proper supersets of earlier versions, i.e. everything that works with one version of MolScript will work with a later version.

Erroneous behaviour (i.e. bugs) may be changed between versions. In v2.1, this applies especially to the implementation of lighting in the Raster3D output mode, which is suboptimal, and should be improved in future versions.

Only in extremely well-founded cases will there be exceptions to this (but see below). However, if any such exceptions are introduced, these will be high-lighted in the documentation.

The reason for giving this statement is to make it possible for other programmers to produce software that automatically generates MolScript input files, which will be valid also for later versions of MolScript.

Note that this policy statement does not refer to the internal implementation details of MolScript, nor to the details of the output file formats. For instance, the procedure definitions in the PostScript output file, or the PROTO's in the VRML 2.0 output file may very well change from one version to the next.

Not an API!

The MolScript software is not an API (Application Programming Interface). The internal features of the MolScript source code are not intended to be used as library routines in other software.

You may modify the MolScript software, or use parts of the code for your own programs. However, all such software is covered by the license agreement, and so cannot be distributed to others without an explicit agreement with Avatar Software AB.

Note that there is no guarantee that the organisation of the source code will be stable in future versions of MolScript. The source code may change drastically between releases. Any modifications or addition you make to the source code will most likely have to be reviewed carefully before upgrading to a new version.

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