psiphi

 

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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

   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

   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. 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

Standard (Mandatory) qualifiers Allowed values Default
[-infile]
(Parameter 1)
Clean protein structure coordinates file Input file Required
-chainnumber Number of the chain for which torsion angles should be calculated Integer 1 or more 1
-startresiduenumber First residue in chain for which torsion angles should be calculated Integer 1 or more 1
-finishresiduenumber Last residue in chain for which torsion angles should be calculated (1 = last residue) Any integer value 1
[-outfile]
(Parameter 2)
Output report file name Report output file <*>.psiphi
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

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    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


  [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    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
//

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, trace, listfile, dbmotif, diffseq, excel, feattable, motif, 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: Tue 15 Jul 2008 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 (d.counsell © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

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

Comments

None