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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML EXPERIMENTAL 970324//EN"><HTML><HEAD><META NAME="GENERATOR" CONTENT="Adobe FrameMaker 5.5/HTML Export Filter"><LINK REL="STYLESHEET" HREF="Manual.css"><TITLE> autoMS</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=3030"> </A><A NAME="33642"> </A><A NAME="marker=14898"> </A>autoMS</H2><P CLASS="Body"><A NAME="pgfId=3034"> </A>Author: Andy Good, Daniel Gschwend</P><P CLASS="Body"><A NAME="pgfId=3048"> </A>autoMS is an extremely useful tool for setting up for <A HREF="Manual.20.html#17338" CLASS="XRef">sphgen</A>. This script converts PDB files to QCPE ms input format, runs a QCPE ms surface calculation, converts the resulting surface to UCSF MS format with <A HREF="Manual.3a.html#22646" CLASS="XRef">reformatms</A>, creates a SYBYL dot file of the surface (if <A HREF="Manual.31.html#28513" CLASS="XRef">ms2dot</A> is available), and prepares an INSPH file for running sphgen. The requirements are only two files: a receptor PDB file, and an <A NAME="marker=15369"> </A>exclude.pdb file. The exclude.pdb file is a subset of the receptor and contains the residues which should not be surfaced in the ms calculation. This file can be created in several ways. The easiest, if sybyl is available, is to select all residues in the receptor within some radius of a known ligand, invert the selection, and write out the file in Brookhaven format as exclude.pdb. One alternative that does not require sybyl is to use <A HREF="Manual.2c.html#12611" CLASS="XRef">get_near_res</A> to locate all receptor atoms or residues within a specified radius of a known ligand and invert the resulting pdb file using <A HREF="Manual.2f.html#18604" CLASS="XRef">invertPDB</A>. </P><P CLASS="Body"><A NAME="pgfId=3050"> </A>Usage: autoMS receptor_PDB_file [surface_density] [probe_radius]</P><P CLASS="Body"><A NAME="pgfId=3052"> </A>where surface_density and probe_radius are optional, defaulting to 3.0 dots/Å2 and 1.4Å, respectively. Note: before using the first time, the directory specification for the dock hierarchy must be updated inside the autoMS script.</P><CENTER><P>?? 快捷鍵說明
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