Per J. Kraulis, MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, Journal of Applied Crystallography (1991) vol 24, pp 946-950.This citation must be given in all publications using images produced with MolScript.
A feature of MolScript is that irregularities in helices and strands are still visible to some degree in the schematic drawings. Especially the helices manage to convey bends and other irregularities without turning ugly. Since only CA-coordinates are used for creating the schematic drawings, even poorly refined structures can give reasonable-looking schematic objects. This may or may not be advantage, depending on one's point of view...
The atom and residue selection mechanism was inspired by a similar facility in the structure refinement program X-PLOR (Brünger 1992).
An orthographic projection is used in all output modes except VRML 2.0 output mode. The projection used in VRML cannot be specified by MolScript; it is entirely dependent on the VRML browser used to display the VRML file.
The success of the MolScript program (more than 2,000 academic licenses, and more than 30 commercial licenses issued by October 1997) shows that there was a great need for such a program. In the years since MolScript was first released (1991), several other similar programs have appeared, which either are designed solely for producing high-quality images of biological macromolecules, or have such output procedures as integral features. For MolScript to remain useful in such competition, novel features and improvements in the software in the light of experience had to be implemented.
The emergence of the VRML 2.0 standard in 1996-1997 for 3D Web applications was an inspiration for creating a new version of MolScript, since it was obvious that the features in MolScript were a very good basis for creating informative and useful VRML representations of molecular structures. The Web has from its start been employed by the molecular biologists and geneticists for sharing data and knowledge, thereby helping to create the new field called bioinformatics. There is a huge potential for the biological structural sciences to use the Web for sharing not only the structural data itself, but also structural knowledge. The VRML 2.0 standard is a good basis for this.
The appearance of the OpenGL standard library and API for high-quality 3D graphics applications in 1993 made it possible to write an interactive-graphics implementation for MolScript which potentially could run on a broad range of computer systems. Also, the off-screen rendering capabilities of many OpenGL implementations made it possible to produce image files directly through MolScript. Since such image files are now a staple of the Web, such a feature would clearly be quite useful.
The previous versions of MolScript were written in Fortran 77. One major problem with this was the lack of a standard dynamic-memory feature in Fortran 77. This argued for re-implementation in another, more modern language.
Considering the various available programming languages, the final
decision was to use ANSI C: it is a small, simple language, with
almost universal and standardized support on all relevant computer
systems. For this application, this outweighs the drawbacks: no
object-oriented features, possible memory leaks using the primitive
memory allocation system, and name-space collision potential. Another
consideration was the availability of many useful software library
packages and utilities in the C language or targeted towards C, which
could be useful. For example, the bison utility from the
GNU project and the
JPEG library from the Independent JPEG
Group.
As part of the reimplementation, the routines that create the graphical objects were clearly separated from the routines that output the objects in a given format. This separation should facilitate future implementation of novel output formats. Also, it makes it easier to ensure that the appearance of the graphical objects is as similar as possible in the different output formats.
Of course, a resourceful and curious person can always look in the source code and figure out what the undocumented commands are. There is nothing to stop you from using them. But beware of their volatile nature!
regex software written by Henry
Spencer, and it has copyright © 1986 University of Toronto. It
has been slightly modified by Per Kraulis.
Ethan Merritt and Mats Dahlberg have contributed to the bug fixes and modifications in v2.0.1 and v2.0.2.
For input and support during the work on version 2.0 of MolScript, I wish to thank Anders Lillienau, Mats Dahlberg, Björn O. Nilsson, Johan Kördel, Michael Åsman, Mats Kihlén, Henrik Fridén, Derek Ogg, Jonas Uppenberg and others at the Structural Chemistry department and other departments of Discovery Research at Pharmacia & Upjohn Inc., Sweden. Robert Esnouf provided input for the separate residue colour feature through his BobScript, a modified version of MolScript.
For input and support during the work on versions 1.0 to 1.4 of MolScript, I thank T. Alwyn Jones, Mats Kihlén, Ylva Lindqvist, Erling Wikman, Hans Eklund, Carl-Ivar Brändén and others at the Department of Molecular Biology, BMC, Uppsala University. This work was supported in part by Nordisk Industrifond and The Swedish Natural Science Research Council (NFR).
The following have contributed bug discoveries, fixes and other suggestions for versions 1.1 - 1.4 of the program: Eric Fauman, Michael Sutcliffe, Paul McLaughlin, Leo Caves, Arne Elofsson.
Ethan A. Merritt wrote the interface to Raster3D in version 1.4 of MolScript.