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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: psiphi
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
psiphi
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Calculates phi and psi torsion angles from protein coordinates

<H2>
    Description
</H2>

<p><b>psiphi</b> reads a clean coordinate file (CCF) of protein
structure coordinates and writes a standard EMBOSS report file of psi
and phi torsion angles in a specified region of a specified
polypeptide chain.  The angles are calculated for each alpha carbon
(CA) atom from the co-ordinates of the mainchain atoms in the two
planes around it.</p>



<H2>
    Algorithm
</H2>

<!-- 
        Algorithms
	  Pseudocode/Vague description/Handwaving/web links to useful pages
  -->


<H2>
    Usage
</H2>

Here is a sample session with <b>psiphi</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>psiphi 1hmp_a.ccf -chainnumber=1 -startresiduenumber=5 -finishresiduenumber=85 </b>
Calculates phi and psi torsion angles from protein coordinates
Output report [1hmp_a.psiphi]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Calculates phi and psi torsion angles from protein coordinates
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     Clean protein structure coordinates file
   -chainnumber        integer    [1] Number of the chain for which torsion
                                  angles should be calculated (Integer 1 or
                                  more)
   -startresiduenumber integer    [1] First residue in chain for which torsion
                                  angles should be calculated (Integer 1 or
                                  more)
   -finishresiduenumber integer    [1] Last residue in chain for which torsion
                                  angles should be calculated (1 = last
                                  residue) (Any integer value)
  [-outfile]           report     [*.psiphi] Output report file name (default
                                  -rformat table)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-infile]<br>(Parameter 1)</td>
<td>infile</td>
<td>Clean protein structure coordinates file</td>
<td>Input file</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-chainnumber</td>
<td>integer</td>
<td>Number of the chain for which torsion angles should be calculated</td>
<td>Integer 1 or more</td>
<td>1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-startresiduenumber</td>
<td>integer</td>
<td>First residue in chain for which torsion angles should be calculated</td>
<td>Integer 1 or more</td>
<td>1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-finishresiduenumber</td>
<td>integer</td>
<td>Last residue in chain for which torsion angles should be calculated (1 = last residue)</td>
<td>Any integer value</td>
<td>1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>report</td>
<td>Output report file name</td>
<td>(default -rformat table)</td>
<td><i>&lt;*&gt;</i>.psiphi</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated report qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rformat2<br>-rformat_outfile</td>
<td>string</td>
<td>Report format</td>
<td>Any string</td>
<td>table</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rname2<br>-rname_outfile</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rextension2<br>-rextension_outfile</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rdirectory2<br>-rdirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -raccshow2<br>-raccshow_outfile</td>
<td>boolean</td>
<td>Show accession number in the report</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rdesshow2<br>-rdesshow_outfile</td>
<td>boolean</td>
<td>Show description in the report</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rscoreshow2<br>-rscoreshow_outfile</td>
<td>boolean</td>
<td>Show the score in the report</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rstrandshow2<br>-rstrandshow_outfile</td>
<td>boolean</td>
<td>Show the nucleotide strand in the report</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rusashow2<br>-rusashow_outfile</td>
<td>boolean</td>
<td>Show the full USA in the report</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rmaxall2<br>-rmaxall_outfile</td>
<td>integer</td>
<td>Maximum total hits to report</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -rmaxseq2<br>-rmaxseq_outfile</td>
<td>integer</td>
<td>Maximum hits to report for one sequence</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<H2>
    Input file format
</H2>

<b>psiphi</b> reads a clean coordinate file (CCF) of protein
structure coordinates.

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: 1hmp_a.ccf</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   1hmp_a
XX
DE   .
XX
OS   .
XX
EX   METHOD xray; RESO 2.50; NMOD 1; NCHN 1; NGRP 0;
XX
CN   [1]
XX
IN   ID A; NR 214; NL 0; NH 0; NE 0;
XX
SQ   SEQUENCE   214 AA;  24120 MW;  8D6FB467 CRC32;
     SPGVVISDDE PGYDLDLFCI PNHYAEDLER VFIPHGLIMD RTERLARDVM KEMGGHHIVA
     LCVLKGGYKF FADLLDYIKA LNRNSDRSIP MTVDFIRLKS YCNDQSTGDI KVIGGDDLST
     LTGKNVLIVE DIIDTGKTMQ TLLSLVRQYN PKMVKVASLL VKRTPRSVGY KPDFVGFEIP
     DKFVVGYALD YNEYFRDLNH VCVISETGKA KYKA
XX
CO   1    1    .    P    1     1     .    .    .    .    .    .    S    SER    N     51.993   53.717   25.698    1.00   37.54    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    1     1     .    .    .    .    .    .    S    SER    CA    52.814   53.824   24.502    1.00   41.16    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    1     1     .    .    .    .    .    .    S    SER    C     51.997   54.081   23.227    1.00   34.87    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    1     1     .    .    .    .    .    .    S    SER    O     50.959   53.486   23.008    1.00   33.66    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    1     1     .    .    .    .    .    .    S    SER    CB    53.743   52.616   24.334    1.00   49.66    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    1     1     .    .    .    .    .    .    S    SER    OG    54.029   52.378   22.957    1.00   53.87    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    2     2     .    .    .    .    .    .    P    PRO    N     52.447   55.004   22.388    1.00   33.37    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    2     2     .    .    .    .    .    .    P    PRO    CA    51.763   55.264   21.128    1.00   33.39    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    2     2     .    .    .    .    .    .    P    PRO    C     52.425   54.401   20.066    1.00   27.66    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    2     2     .    .    .    .    .    .    P    PRO    O     52.291   54.590   18.851    1.00   28.29    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    2     2     .    .    .    .    .    .    P    PRO    CB    52.034   56.746   20.799    1.00   35.05    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    2     2     .    .    .    .    .    .    P    PRO    CG    53.162   57.218   21.727    1.00   34.02    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    2     2     .    .    .    .    .    .    P    PRO    CD    53.218   56.209   22.865    1.00   33.44    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    3     3     .    .    .    .    .    .    G    GLY    N     53.208   53.487   20.565    1.00   20.99    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    3     3     .    .    .    .    .    .    G    GLY    CA    53.980   52.705   19.675    1.00   22.46    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    3     3     .    .    .    .    .    .    G    GLY    C     54.958   53.659   19.030    1.00   16.09    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    3     3     .    .    .    .    .    .    G    GLY    O     55.205   54.766   19.512    1.00   20.19    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    4     4     .    .    .    .    .    .    V    VAL    N     55.506   53.240   17.948    1.00   10.04    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    4     4     .    .    .    .    .    .    V    VAL    CA    56.416   54.088   17.282    1.00   15.89    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    4     4     .    .    .    .    .    .    V    VAL    C     55.625   55.088   16.453    1.00   17.74    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    4     4     .    .    .    .    .    .    V    VAL    O     54.828   54.675   15.629    1.00   15.36    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    4     4     .    .    .    .    .    .    V    VAL    CB    57.332   53.194   16.451    1.00   18.65    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    4     4     .    .    .    .    .    .    V    VAL    CG1   58.444   53.988   15.754    1.00   18.67    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    4     4     .    .    .    .    .    .    V    VAL    CG2   57.922   52.084   17.346    1.00   13.73    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    5     5     .    .    .    .    .    .    V    VAL    N     55.799   56.415   16.693    1.00   25.51    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    5     5     .    .    .    .    .    .    V    VAL    CA    55.049   57.431   15.929    1.00   20.42    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    5     5     .    .    .    .    .    .    V    VAL    C     55.655   57.849   14.605    1.00   21.66    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    5     5     .    .    .    .    .    .    V    VAL    O     56.846   58.112   14.504    1.00   31.38    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    5     5     .    .    .    .    .    .    V    VAL    CB    54.697   58.659   16.709    1.00   16.90    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    5     5     .    .    .    .    .    .    V    VAL    CG1   54.131   59.664   15.699    1.00   19.06    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    5     5     .    .    .    .    .    .    V    VAL    CG2   53.640   58.304   17.738    1.00   14.10    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    6     6     .    .    .    .    .    .    I    ILE    N     54.810   57.974   13.593    1.00   20.18    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00


<font color=red>  [Part of this file has been deleted for brevity]</font>

CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    N     46.988   51.534   -7.357    1.00   39.61    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    CA    45.791   51.590   -6.554    1.00   41.75    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    C     44.610   51.650   -7.444    1.00   44.10    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    O     43.570   51.024   -7.222    1.00   47.08    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    CB    45.764   52.773   -5.656    1.00   41.31    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    CG    44.785   52.588   -4.531    1.00   40.21    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    CD    43.819   53.733   -4.515    1.00   44.44    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    CE    44.335   54.889   -5.365    1.00   49.29    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    209   209   .    .    .    .    .    .    K    LYS    NZ    44.965   55.969   -4.577    1.00   50.32    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    210   210   .    .    .    .    .    .    A    ALA    N     44.813   52.416   -8.475    1.00   43.71    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    210   210   .    .    .    .    .    .    A    ALA    CA    43.787   52.546   -9.446    1.00   41.88    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    210   210   .    .    .    .    .    .    A    ALA    C     43.831   51.390  -10.416    1.00   39.92    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    210   210   .    .    .    .    .    .    A    ALA    O     42.865   51.153  -11.085    1.00   48.09    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    210   210   .    .    .    .    .    .    A    ALA    CB    43.842   53.898  -10.151    1.00   40.52    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    N     44.935   50.644  -10.479    1.00   36.47    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    CA    45.123   49.543  -11.471    1.00   40.27    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    C     44.659   48.140  -11.033    1.00   41.97    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    O     44.458   47.243  -11.847    1.00   40.79    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    CB    46.560   49.545  -12.092    1.00   37.63    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    CG    47.140   48.161  -12.390    1.00   33.69    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    CD    48.551   47.914  -11.838    1.00   29.45    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    CE    49.678   48.306  -12.772    1.00   25.87    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    211   211   .    .    .    .    .    .    K    LYS    NZ    50.909   47.533  -12.545    1.00   26.93    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    N     44.581   47.951   -9.718    1.00   44.88    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CA    44.160   46.704   -9.076    1.00   42.88    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    C     42.720   46.902   -8.639    1.00   46.06    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    O     42.495   47.283   -7.493    1.00   49.33    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CB    45.026   46.454   -7.772    1.00   35.96    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CG    46.478   46.111   -8.046    1.00   26.75    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CD1   46.745   45.100   -8.965    1.00   27.47    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CD2   47.556   46.816   -7.509    1.00   18.91    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CE1   48.037   44.766   -9.366    1.00   24.84    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CE2   48.858   46.511   -7.909    1.00   22.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    CZ    49.103   45.446   -8.787    1.00   25.50    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    212   212   .    .    .    .    .    .    Y    TYR    OH    50.377   45.086   -9.149    1.00   23.28    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    N     41.703   46.726   -9.463    1.00   48.75    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    CA    40.474   47.096   -8.795    1.00   60.15    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    C     39.248   46.226   -8.710    1.00   61.60    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    O     39.218   45.071   -9.141    1.00   68.05    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    CB    40.203   48.573   -8.682    1.00   73.04    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    CG    39.555   49.149   -9.926    1.00   82.29    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    CD    40.446   49.096  -11.156    1.00   88.26    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    CE    39.662   49.334  -12.441    1.00   93.01    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    213   213   .    .    .    .    .    .    K    LYS    NZ    40.403   50.145  -13.447    1.00   95.26    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    214   214   .    .    .    .    .    .    A    ALA    N     38.248   46.846   -8.067    1.00   57.39    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    214   214   .    .    .    .    .    .    A    ALA    CA    36.910   46.306   -7.804    1.00   53.48    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    214   214   .    .    .    .    .    .    A    ALA    C     35.963   46.427   -8.990    1.00   54.67    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    214   214   .    .    .    .    .    .    A    ALA    O     36.467   46.591  -10.145    1.00   53.03    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    214   214   .    .    .    .    .    .    A    ALA    CB    36.263   46.991   -6.605    1.00   49.58    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
CO   1    1    .    P    214   214   .    .    .    .    .    .    A    ALA    OXT   34.731   46.398   -8.724    1.00   56.06    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
//
</pre>
</td></tr></table><p>





<H2>
    Output file format
</H2>

<p>

The output is a standard EMBOSS report file. 

<p>

The results can be output in one of several styles by using the
command-line qualifier <tt>-rformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif,
diffseq, draw, restrict, excel, feattable, motif, nametable, regions,
seqtable, simple, srs, table, tagseq.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.

<p>

By default <b>psiphi</b> writes a 'table' format report file.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: 1hmp_a.psiphi</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: psiphi
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: psiphi
#    [-infile] ../../data/1hmp_a.ccf
#    -chainnumber 1
#    -startresiduenumber 5
#    -finishresiduenumber 85
# Report_format: table
# Report_file: 1hmp_a.psiphi
########################################

#=======================================
#
# Sequence: 1hmp_a     from: 1   to: 214
# HitCount: 81
#
# Chain: 1
#
#=======================================

  Start     End   Score     phi     psi
      5       5     0.0  -85.52  137.17
      6       6     0.0 -124.99   85.24
      7       7     0.0  -43.12  147.11
      8       8     0.0  -48.31  -29.94
      9       9     0.0  -88.16   -2.35
     10      10     0.0  -52.85  130.05
     11      11     0.0  -93.40   -4.97
     12      12     0.0   79.02 -136.70
     13      13     0.0 -149.38  150.69
     14      14     0.0  -84.79  150.76
     15      15     0.0  -46.26  -29.65
     16      16     0.0  -58.90  -26.97
     17      17     0.0  -93.04  -13.65
     18      18     0.0 -121.01  177.67
     19      19     0.0  -90.34  123.35
     20      20     0.0 -137.24  150.01
     21      21     0.0  -60.85  141.25
     22      22     0.0  -68.94  -27.08
     23      23     0.0  -71.26   -5.87
     24      24     0.0 -124.07   13.09
     25      25     0.0  -79.54   22.76
     26      26     0.0 -145.15  -13.78
     27      27     0.0  -95.38    4.02
     28      28     0.0 -129.20  149.61
     29      29     0.0  -90.42  -47.84
     30      30     0.0 -162.69  160.59
     31      31     0.0  -75.67  128.31
     32      32     0.0  -96.18  -51.71


<font color=red>  [Part of this file has been deleted for brevity]</font>

     38      38     0.0  -48.48  -63.46
     39      39     0.0  -38.67  -55.32
     40      40     0.0  -62.06  -37.43
     41      41     0.0  -66.93  -47.14
     42      42     0.0  -55.67  -36.42
     43      43     0.0  -63.04  -44.39
     44      44     0.0  -53.57  -57.37
     45      45     0.0  -44.65  -49.45
     46      46     0.0  -51.29  -42.54
     47      47     0.0  -66.60  -39.52
     48      48     0.0  -63.88  -48.01
     49      49     0.0  -56.50  -52.92
     50      50     0.0  -62.39  -18.62
     51      51     0.0  -56.19  -46.58
     52      52     0.0  -86.42  -51.81
     53      53     0.0  -88.19  -25.17
     54      54     0.0  -56.43  151.52
     55      55     0.0   85.66    9.25
     56      56     0.0 -139.15  162.01
     57      57     0.0  -65.45  110.45
     58      58     0.0 -101.25  138.36
     59      59     0.0 -105.46  112.70
     60      60     0.0  -93.70  115.62
     61      61     0.0 -108.38  131.59
     62      62     0.0 -109.96  130.63
     63      63     0.0  -94.00  109.57
     64      64     0.0  -93.72   67.41
     65      65     0.0  -65.62 -102.57
     66      66     0.0 -109.14   11.70
     67      67     0.0 -170.15  178.49
     68      68     0.0 -125.12  -30.99
     69      69     0.0  -36.99  -53.96
     70      70     0.0  -62.26  -46.94
     71      71     0.0  -50.46  -58.23
     72      72     0.0  -51.09  -52.57
     73      73     0.0  -56.83  -50.75
     74      74     0.0  -55.14  -51.03
     75      75     0.0  -54.01  -32.78
     76      76     0.0  -64.26  -33.38
     77      77     0.0  -73.24  -38.25
     78      78     0.0  -67.12  -50.61
     79      79     0.0  -47.17  -56.48
     80      80     0.0  -49.34  -24.22
     81      81     0.0  -90.53  -27.37
     82      82     0.0  -79.04    3.07
     83      83     0.0  -72.14  -34.64
     84      84     0.0  -78.17   -5.83
     85      85     0.0  -70.69  142.19

#---------------------------------------
#---------------------------------------
</pre>
</td></tr></table><p>





<H2>
    Data files
</H2>


<H2>
    Notes
</H2>


<p>Clean coordinate file (CCF) of protein structure coordinates are
generated by running pdbparse (in the 'structure' EMBASSY package) on
a PDB file.</p>






<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>
Damian Counsell formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.




<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


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