                                   psiphi



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Calculates phi and psi torsion angles from protein coordinates

Description

   psiphi 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.

Algorithm

Usage

   Here is a sample session with psiphi


% psiphi 1hmp_a.ccf -chainnumber=1 -startresiduenumber=5 -finishresiduenumber=85

Calculates phi and psi torsion angles from protein coordinates
Output report [1hmp_a.psiphi]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Calculates phi and psi torsion angles from protein coordinates
Version: EMBOSS:6.4.0.0

   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


Input file format

   psiphi reads a clean coordinate file (CCF) of protein structure
   coordinates.

  Input files for usage example

  File: 1hmp_a.ccf

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    C
A    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    C
B    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    O
G    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    C
A    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    C
B    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    C
G    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    C
D    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    C
A    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    C
A    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    C
B    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    C
G1   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    C
G2   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    C
A    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    C
B    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    C
G1   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    C
G2   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


  [Part of this file has been deleted for brevity]

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    C
A    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    C
B    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    C
G    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    C
D    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    C
E    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    N
Z    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    C
A    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    C
B    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    C
A    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    C
B    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    C
G    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    C
D    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    C
E    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    N
Z    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    C
A    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    C
B    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    C
G    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    C
D1   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    C
D2   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    C
E1   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    C
E2   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    C
Z    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    O
H    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    C
A    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    C
B    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    C
G    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    C
D    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    C
E    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    N
Z    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    C
A    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    C
B    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    O
XT   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
//

Output file format

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, 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.

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default psiphi writes a 'table' format report file.

  Output files for usage example

  File: 1hmp_a.psiphi

########################################
# Program: psiphi
# Rundate: Fri 15 Jul 2011 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


  [Part of this file has been deleted for brevity]

     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

#---------------------------------------
#---------------------------------------

Data files

Notes

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

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description

Author(s)

   Damian Counsell formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
