molscript's Introduction

MolScript v2.1.2

Copyright (C) 1997-1998 Per J. Kraulis

MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.

The documentation is at http://pekrau.github.io/MolScript/.

Background

MolScript has for a long time been a standard tool in the science of macromolecular structures. The paper describing it appears as number 82 in the list of the Nature feature article "The Top 100 Papers. Nature explores the most-cited research of all time" by Richard Van Noorden, Brendan Maher & Regina Nuzzo published 30 Oct 2014.

I have written a blog post MolScript: A story of success and failure, describing the history behind its rise and fall.

Open Source

MolScript is now available under the MIT license from this GitHub repository. I have for a long time intended to make MolScript Open Source, but never got around to it. The Nature Top-100-list did the trick of pushing me into action.

Version 2.1.2

The first version of MolScript (written in Fortran 77) was released in 1991, and its current version (2.1.2, written in C) in 1998.

Please be aware that no changes have been made to the code since 1998. In particular, the Makefile for the executable including OpenGL support is not up to scratch. It needs updating. If anyone is willing to help, I would much appreciate it.

I have tested the Makefile.basic file, which builds an executable with support for PostScript, Raster3D and VRML. It works, at least on Ubuntu 12.04. I have also verified that the Raster3D software (v3.0) still works with MolScript.

Future plans

I have very little time to work on MolScript currently. Other projects are more pressing. If anyone is willing to "take over" (i.e. fork) and continue developing MolScript, I would be very pleased.

Here are some possible items for a roadmap for future development of MolScript:

Fix the OpenGL implementation, with a working Makefile.
Prepare a proper Debian package for easier installation.
Add a proper interactive interface to the OpenGL implementation. The script language was nice once upon a time, but today it must be considered as user-hostile and cumbersome.
Write an implementation to produce X3D, the successor to the VRML format for 3D objects on the web.
Write a WebGL implementation.
Set up a web service producing images from input scripts using MolScript.

Reference

Per J. Kraulis
MOLSCRIPT: a program to produce both detailed and schematic plots of
protein structures.
J. Appl. Cryst. (1991) 24, 946-950

This paper is now available under Open Access: PDF

DOI:10.1107/S0021889891004399

Entry at J. Appl. Cryst. web site

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molscript's Issues

Missing header file glutbitmap.h

It is used here: https://github.com/pekrau/MolScript/blob/master/code/clib/ogl_bitmap_character.c#L26 but isn't available in the project.

JSON input?

Or YAML. For web service.

Build fails: uses the opaque type 'struct png_struct_def'

png_img.c:72:22: error: incomplete definition of type 'struct png_struct_def'
  if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp");
              ~~~~~~~^

poor bond detection with hydrogens

MolScript by default connects adjacent hydrogens, like on methyl groups. This can be seen in many figures on the RCSB PDB website, e.g.:

http://www.rcsb.org/pdb/explore/images.do?structureId=4RWC
http://www.rcsb.org/pdb/explore/images.do?structureId=1AY3
http://www.rcsb.org/pdb/explore/images.do?structureId=3fw1
http://www.rcsb.org/pdb/explore/images.do?structureId=4rwb
http://www.rcsb.org/pdb/explore/images.do?structureId=4p3r
http://www.rcsb.org/pdb/explore/images.do?structureId=2A31

Pull request #2 addresses this issue.

Wrong format specification

clang-6 prints this warning:

eps_img.c:122:34: warning: cc -O1 -ansi -Iclib -DOPENGL_SUPPORT -I/glut/include -DIMAGE_SUPPORT -DJPEG_SUPPORT -I/jpeg -DPNG_SUPPORT -I/libpng -I/zlib -DGIF_SUPPORT -I/gd -fno-omit-frame-pointer -isystem /usr/local/include  -c -o jpeg_img.o jpeg_img.c
format specifies type 'unsigned short' but the argument has type 'char' [-Wformat]
      fprintf (outfile, "%02hx", *pix++);
                         ~~~~~   ^~~~~~
                         %02hhx

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