MolScript is a program for creating molecular graphics in the form of PostScript plot files. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. Color, grayscale, shading and depth cueing can be applied to the various graphical objects.
The QUANTA interface to MolScript generates the input script and coordinate files to reproduce as nearly as possible the current representation. Objects rendered include bonds, solid models, hydrogen bonds, distance monitors, labels and atom IDs.
The interface is accessed by using the function Plot Molecules Æ Generate on the File menu. This displays the usual Setup Hard Copy Plot of Molecules dialog, which now includes an extra radio button, MolScript Plot. When this is used, a new dialog box is displayed containing the MolScript interface options.
The following is a brief description of the various options:
The interface will produce two files, filename.pdb containing the molecular coordinates, and filename.in containing the MolScript commands. Running the program will produce the PostScript file filename.ps or filename.eps.
Allows the choice of normal (.ps) or Encapsulated PostScript (.eps).
This is used to control the maximum bond distance allowed in ball-and-stick plots. The default, 2.1 Å is suitable for proteins containing disulfide bridges but no hydrogen atoms; if hydrogen atoms are present a smaller value will be needed to prevent the hydrogen atoms being bonded together. Vector bonds are generated using the LINE command so that the exact bonding generated by QUANTA can be replicated regardless of this setting.
MolScript allows for optional smoothing of thin ribbons. This can make for a clearer diagram, but should be avoided if sidechains are also displayed.
This can sometimes make for a clearer diagram.
Changes the color settings to be optimized for the drawing of solid models. Note - the plot will always have a white background regardless of the QUANTA background color.
Allows the input files to be retained - expert users may wish to manually adjust the input and rerun molscript. If this option is unchecked, then the input files will be deleted if MolScript is run successfully.
This option causes the resulting PostScript plot to be displayed using the xpsview viewing program. This requires that xpsview can be found in the user's path or that there is an alias pointing to it.
If both solid models and vector bonds are displayed on screen, then both will be included in the MolScript plot. Remember that vector bonds can be rapidly toggled using function key <F10>, if the default key bindings are set up. Otherwise enter the commands HIDE BOND and SHOW BOND.
When the OK button is hit, the input files are created and molscript will be run if it can be found in the user's path or if there is an alias pointing to it.
The MolScript program must be obtained from its author, Dr. Per Kraulis.
Per Kraulis, Ph.D
Pharmacia & Upjohn, Inc.
PPC Sweden Research, N62:5
S-112 87 Stockholm
SWEDEN
phone: +46 (8) 695 78 34
fax: +46 (8) 695 40 82
e-mail: krpx@sgikrpe.sto.se.pnu.com
or p.j.kraulis@bioc.cam.ac.uk
or molscript@bioc.cam.ac.uk
The software is provided under license - details from Per Kraulis.
In publications, you must refer to:
Per J. Kraulis "MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures" Journal of Applied Crystallography 24 946-950 (1991).