SCRIPT program

Figure 15.6. Kinemage built-in scripts page of PREKIN program. Build-in scripts program for converting molecule.pdb file into molecule.kin file according to the selection(s) for structural features to be displayed/manipulated. To terminate the selection, click OK button. For more than one selection (structural features), click restart this Pass button.

Figure 7 The nine possible conformational diagrams for a six-membered ring in the SCRIPT program. The torsional angles of the ring bonds are only defined by their sign ( + /—) or zero (0) for a planar bond.

Figure 7 Cyclohexane conformational diagrams used by the Script program.

RasMol contains many excellent output formats and can be used with the Mol-script program (Kraulis, 1991) to make wonderful PostScript ribbon diagrams for publication. To make optimal use of RasMol, however, one must master its command-line language, a familiar feature of many legacy three-dimensional structure programs. 

Pedretti, A.L., Villa, G., and Vistoli, G. 2004. VEGA—An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J. Comput. Aided Mol. Des. 18 167-173. 

One significant characteristic of the program is the Command Line. Hereby, the visualization of the molecules is directed in the viewer with commands from a script language. The scripts, such as loop or batch files, can be saved, lutp //openrasmoi.org... 

The program comes with its own job queue system. Jobs are submitted to this queue via a script, which can be edited to utilize third-party batch-queuing systems instead. 

Crystal (we tested Crystal 98 1.0) is a program for ah initio molecular and band-structure calculations. Band-structure calculations can be done for systems that are periodic in one, two, or three dimensions. A separate script, called LoptCG, is available to perform optimizations of geometry or basis sets. 

The ASCII input file includes elements of a scripting language. Thus, the input can contain variables, loops, and procedures. This is one of the aspects of the program that makes it possible to do very complex calculations. The documentation describes the input options, but does not discuss when and why they should be used. The user must have a solid understanding of ah initio theory in order to correctly utilize many of the functions in this program. It is very powerful, but not for beginners. 

FieldNotes user verification can be conducted by following the SOP written by Astrix, which can be downloaded from the Astrix Web site. The SOP contains a script that is typed into the computer system. If the printout matches the SOP script, then verification is complete. A record of this must be placed in the facility archive. This verification process takes 1 h or less. For FieldNotes, calculations are not verified at the field site since the manufacturer feels that the software developer and the sponsors have performed adequate validation of these calculations previously. This may, therefore, require a visit to the sponsor or to the manufacturer to confirm that this important step of the validation process has been completed and is adequately documented. By following the Astrix SOP, the user is simply ensuring that the program operates on their system(s). The SOP script must be typed in exactly as written in order to confirm the printout accuracy. QA must ensure that the verification documentation is properly archived. Just as with any other SOP, this SOP must be approved in writing by field site management to comply with GLP. 

Methods and scripts are software resources that help the operator to set up complex investigations without concentrating on the basic requirements. Furthermore, these software modules can handle the interaction between various parts of the NMR software package, to support the geometry editor, auto adjustments, routine parameter handling or pulse handling program. 

In this book, input scripts for running the various programs are set in a typewriter typeface. Unless a script is marked as a continuation of the previous script, you should start the program anew or type reset to clear your previous configuration. 

I chose to use this software for reasons that extend beyond familiarity and prejudice the programs are interactive and take simple commands as input. As such, I can include within the text of this book scripts that in a few lines show the precise steps taken to calculate each result. Readers can, of course, reproduce the calculations by using any of a number of other modeling programs, such as those listed in Appendix 1. Following the steps shown in the text, they should be able to construct input in the format recognized by the chosen program. 

Few systems genuinely allow end users to make arbitrary extensions those that allow it must provide a programming or scripting language of some sort. Normally there is some restriction all the additions fit within a framework. An example is a computer aided design (CAD) system, in which new kinds of mechanical parts can be added and the users... 

The core of the current version of Candid is implemented in standard Fortran-77 and has been built upon the data structures and into the framework of the user interface of the program Dyana. The standard schedule and parameters for a complete automated structure determination with Candid and Dyana are specified in a script written in the interpreted command language Inclan that gives the user high flexibility in the way automated structure determination is performed without the need to modify the compiled core part of Candid [26]. 

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