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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>do_dssp</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>
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  15 <H3>Description</H3>
  16 <p>
  17 <tt>do_dssp</tt>
  18 reads a trajectory file and computes the secondary structure for
  19 each time frame
  20 calling the dssp program. If you do not have the dssp program,
  21 get it from http://swift.cmbi.ru.nl/gv/dssp. <tt>do_dssp</tt> assumes
  22 that the dssp executable is located in
  23 <tt>/usr/local/bin/dssp</tt>. If this is not the case, then you should
  24 set an environment variable <tt>DSSP</tt> pointing to the dssp
  25 executable, e.g.: <p>
  26 <tt>setenv DSSP /opt/dssp/bin/dssp</tt><p>
  27 Since version 2.0.0, dssp is invoked with a syntax that differs
  28 from earlier versions. If you have an older version of dssp,
  29 use the <tt>-ver</tt> option to direct do_dssp to use the older syntax.
  30 By default, do_dssp uses the syntax introduced with version 2.0.0.
  31 Even newer versions (which at the time of writing are not yet released)
  32 are assumed to have the same syntax as 2.0.0.<p>
  33 The structure assignment for each residue and time is written to an
  34 <tt>.<a href="xpm.html">xpm</a></tt> matrix file. This file can be visualized with for instance
  35 <tt>xv</tt> and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.
  36 Individual chains are separated by light grey lines in the <tt>.<a href="xpm.html">xpm</a></tt> and
  37 postscript files.
  38 The number of residues with each secondary structure type and the
  39 total secondary structure (<tt>-sss</tt>) count as a function of
  40 time are also written to file (<tt>-sc</tt>).<p>
  41 Solvent accessible surface (SAS) per residue can be calculated, both in
  42 absolute values (A^2) and in fractions of the maximal accessible
  43 surface of a residue. The maximal accessible surface is defined as
  44 the accessible surface of a residue in a chain of glycines.
  45 <b>Note</b> that the program <tt><a href="g_sas.html">g_sas</a></tt> can also compute SAS
  46 and that is more efficient.<p>
  47 Finally, this program can dump the secondary structure in a special file
  48 <tt>ssdump.<a href="dat.html">dat</a></tt> for usage in the program <tt><a href="g_chi.html">g_chi</a></tt>. Together
  49 these two programs can be used to analyze dihedral properties as a
  50 function of secondary structure type.
  51 <P>
  52 <H3>Files</H3>
  53 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  54 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  55 <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>
  56 <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> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
  57 <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>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-ssdump</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">  ssdump.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-map</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="map.html">      ss.map</a></tt> </TD><TD> Input, Lib. </TD><TD> File that maps matrix data to colors </TD></TR>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">      ss.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-sc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  scount.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    area.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-ta</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> totarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-aa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">averarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  65 </TABLE>
  66 <P>
  67 <H3>Other options</H3>
  68 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  69 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  70 <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>
  71 <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>
  72 <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>
  73 <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>
  74 <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>
  75 <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>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
  78 <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>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-sss</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>HEBT</tt> </TD><TD> Secondary structures for structure count </TD></TD>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-ver</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> DSSP major version. Syntax changed with version 2 </TD></TD>
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