share/html/online/g_helixorient.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>g_helixorient</TITLE>
   4 <LINK rel=stylesheet href="style.css" type="text/css">
   5 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
   6 <TABLE WIDTH="98%" NOBORDER >
   7 <TR><TD WIDTH=400>
   8 <TABLE WIDTH=400 NOBORDER>
   9 <TD WIDTH=116>
  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_helixorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 <tt>g_helixorient</tt> calculates the coordinates and direction of the average
  18 axis inside an alpha helix, and the direction/vectors of both the
  19 C&alpha; and (optionally) a sidechain atom relative to the axis.<p>
  20 As input, you need to specify an index group with C&alpha; atoms
  21 corresponding to an &alpha;-helix of continuous residues. Sidechain
  22 directions require a second index group of the same size, containing
  23 the heavy atom in each residue that should represent the sidechain.<p>
  24 <b>Note</b> that this program does not do any fitting of structures.<p>
  25 We need four C&alpha; coordinates to define the local direction of the helix
  26 axis.<p>
  27 The tilt/rotation is calculated from Euler rotations, where we define
  28 the helix axis as the local <it>x</it>-axis, the residues/C&alpha; vector as <it>y</it>, and the
  29 <it>z</it>-axis from their cross product. We use the Euler Y-Z-X rotation, meaning
  30 we first tilt the helix axis (1) around and (2) orthogonal to the residues
  31 vector, and finally apply the (3) rotation around it. For debugging or other
  32 purposes, we also write out the actual Euler rotation angles as <tt>theta[1-3].<a href="xvg.html">xvg</a></tt>
  33 <P>
  34 <H3>Files</H3>
  35 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  36 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  37 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  38 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  39 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-oaxis</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">helixaxis.dat</a></tt> </TD><TD> Output </TD><TD> Generic data file </TD></TR>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-ocenter</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">  center.dat</a></tt> </TD><TD> Output </TD><TD> Generic data file </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-orise</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    rise.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-oradius</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  radius.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-otwist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   twist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-obending</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bending.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-otilt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    tilt.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-orot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rotation.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  48 </TABLE>
  49 <P>
  50 <H3>Other options</H3>
  51 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  52 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sidechain</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate sidechain directions relative to helix axis too. </TD></TD>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-[no]incremental</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate incremental rather than total rotation/tilt. </TD></TD>
  62 </TABLE>
  63 <P>
  64 <hr>
  65 <div ALIGN=RIGHT>
  66 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  67 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
  68 </div>
  69 </BODY>