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