<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <!--**************************************************************************** * * * Viewmol * * * * N O D E 5 . H T M L * * * * Copyright (c) Joerg-R. Hill, October 2003 * * * ******************************************************************************** *--> <html> <head> <title>5 Synopsis</title> <META NAME="description" CONTENT="5 Synopsis"> <META NAME="keywords" CONTENT="viewmol"> <META NAME="resource-type" CONTENT="document"> <META NAME="distribution" CONTENT="global"> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <link rel="STYLESHEET" href="viewmol.css"> <link rel="first" href="viewmol.html"> </head> <body> <H1><A NAME="SECTION000500000000000000000"> 5 Synopsis</A> </H1> V<SMALL>IEWMOL</SMALL> can be called as follows: <P> <dl><dd><pre class="verbatim"> viewmol [[-bio | -dmol | -gamess | -gauss | -gulp | -mopac | -pdb | -pqs | -tm | -tmmsi | -vamp] file] </pre></dl> <P> V<SMALL>IEWMOL</SMALL> has an automatic file format detection algorithm build in and should be able to identify output files of the programs supported without user intervention. V<SMALL>IEWMOL</SMALL> will also run Python scripts given on the command line when the Python script has the string <code>python</code> within the first 1024 characters (this is usually the case if the script starts with the common <code>#!/usr/local/bin/python</code> or similar first line). If V<SMALL>IEWMOL</SMALL> is called without parameters it will bring up a file selection box to select the file to be viewed. <P> If the option <code>-bio</code> is used the file name of a D<SMALL>ISCOVER</SMALL> file has to be specified. One can use the <code>.car</code>, the <code>.cor</code>, or the <code>.arc</code> file of D<SMALL>ISCOVER</SMALL>. V<SMALL>IEWMOL</SMALL> also looks for a file with the extension <code>.hessian</code> and tries to read the vibrational spectrum from it, if it was found. <P> If the option <code>-dmol</code> is used the file name of a DM<SMALL>OL/</SMALL>DS<SMALL>OLID/</SMALL>DM<SMALL>OL</SMALL><SUP>3</SUP> output file has to be specified. <P> If the option <code>-gamess</code> is used the file name of a G<SMALL>AMESS</SMALL> output file has to be specified. <P> If the option <code>-gauss</code> is used the file name of a G<SMALL>AUSSIAN 9X</SMALL> output file has to be specified. <P> If the option <code>-gulp</code> is used the file name of a GULP output file has to be specified. <P> If the option <code>-mopac</code> is used the file name of a M<SMALL>OPAC</SMALL> output file has to be specified. V<SMALL>IEWMOL</SMALL> also looks for a file with the extension <code>.gpt</code> and reads information about basis sets and MOs from it, if it was found. <P> If the option <code>-pdb</code> is used the file name of a PDB file has to be specified. <P> If the option <code>-pqs</code> is used the file name of a PQS output file has to be specified. <P> If the options <code>-tm</code> or <code>-tmmsi</code> are used the file name of a T<SMALL>URBOMOLE</SMALL> file containing at least the data group <code>$coord</code> has to be specified. <code>-tm</code> reads the original T<SMALL>URBOMOLE</SMALL> output while <code>-tmmsi</code> allows V<SMALL>IEWMOL</SMALL> to read T<SMALL>URBOMOLE</SMALL> outputs from the T<SMALL>URBOMOLE</SMALL> version distributed by Accelrys (the only difference is the ordering of the normal modes in the <code>control</code> file). <P> If the option <code>-vamp</code> is used the file name of a Vamp output file has to be specified. V<SMALL>IEWMOL</SMALL> also looks for a file with the extension <code>.gpt</code> and reads information about basis sets and MOs from it, if it was found. <P> <p><hr> <ADDRESS> <a href="mailto:joehill@users.sourceforge.net"><i>Jörg-Rüdiger Hill</i></a> Fri Oct 31 14:19:21 CET 2003 </ADDRESS> </BODY> </HTML>