
                                  psiphi 



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=8
5 
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

Input file format

   psiphi reads ...

  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

   psiphi outputs ...

  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
