Tehdyt toimenpiteet
|
psiphi |
Wiki
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Function
Calculates phi and psi torsion angles from protein coordinatesDescription
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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-infile] (Parameter 1) |
infile | Clean protein structure coordinates file | Input file | Required |
| -chainnumber | integer | Number of the chain for which torsion angles should be calculated | Integer 1 or more | 1 |
| -startresiduenumber | integer | First residue in chain for which torsion angles should be calculated | Integer 1 or more | 1 |
| -finishresiduenumber | integer | Last residue in chain for which torsion angles should be calculated (1 = last residue) | Any integer value | 1 |
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat table) | <*>.psiphi |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-outfile" associated report qualifiers | ||||
| -rformat2 -rformat_outfile |
string | Report format | Any string | table |
| -rname2 -rname_outfile |
string | Base file name | Any string | |
| -rextension2 -rextension_outfile |
string | File name extension | Any string | |
| -rdirectory2 -rdirectory_outfile |
string | Output directory | Any string | |
| -raccshow2 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N |
| -rdesshow2 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N |
| -rscoreshow2 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | Y |
| -rstrandshow2 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y |
| -rusashow2 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N |
| -rmaxall2 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 |
| -rmaxseq2 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
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, 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 © emboss.open-bio.org) not to the original author.