psiphi Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Calculates phi and psi torsion angles from protein coordinates Description psiphi reads a clean coordinate file (CCF) of protein structure coordinates and writes a standard EMBOSS report file of psi and phi torsion angles in a specified region of a specified polypeptide chain. The angles are calculated for each alpha carbon (CA) atom from the co-ordinates of the mainchain atoms in the two planes around it. Algorithm Usage Here is a sample session with psiphi % psiphi 1hmp_a.ccf -chainnumber=1 -startresiduenumber=5 -finishresiduenumber=85 Calculates phi and psi torsion angles from protein coordinates Output report [1hmp_a.psiphi]: Go to the input files for this example Go to the output files for this example Command line arguments Calculates phi and psi torsion angles from protein coordinates Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-infile] infile Clean protein structure coordinates file -chainnumber integer [1] Number of the chain for which torsion angles should be calculated (Integer 1 or more) -startresiduenumber integer [1] First residue in chain for which torsion angles should be calculated (Integer 1 or more) -finishresiduenumber integer [1] Last residue in chain for which torsion angles should be calculated (1 = last residue) (Any integer value) [-outfile] report [*.psiphi] Output report file name (default -rformat table) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -rformat2 string Report format -rname2 string Base file name -rextension2 string File name extension -rdirectory2 string Output directory -raccshow2 boolean Show accession number in the report -rdesshow2 boolean Show description in the report -rscoreshow2 boolean Show the score in the report -rstrandshow2 boolean Show the nucleotide strand in the report -rusashow2 boolean Show the full USA in the report -rmaxall2 integer Maximum total hits to report -rmaxseq2 integer Maximum hits to report for one sequence General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format psiphi reads a clean coordinate file (CCF) of protein structure coordinates. Input files for usage example File: 1hmp_a.ccf ID 1hmp_a XX DE . XX OS . XX EX METHOD xray; RESO 2.50; NMOD 1; NCHN 1; NGRP 0; XX CN [1] XX IN ID A; NR 214; NL 0; NH 0; NE 0; XX SQ SEQUENCE 214 AA; 24120 MW; 8D6FB467 CRC32; SPGVVISDDE PGYDLDLFCI PNHYAEDLER VFIPHGLIMD RTERLARDVM KEMGGHHIVA LCVLKGGYKF FADLLDYIKA LNRNSDRSIP MTVDFIRLKS YCNDQSTGDI KVIGGDDLST LTGKNVLIVE DIIDTGKTMQ TLLSLVRQYN PKMVKVASLL VKRTPRSVGY KPDFVGFEIP DKFVVGYALD YNEYFRDLNH VCVISETGKA KYKA XX CO 1 1 . P 1 1 . . . . . . S SER N 51.993 53.717 25.698 1.00 37.54 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . S SER C A 52.814 53.824 24.502 1.00 41.16 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . S SER C 51.997 54.081 23.227 1.00 34.87 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . S SER O 50.959 53.486 23.008 1.00 33.66 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . S SER C B 53.743 52.616 24.334 1.00 49.66 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . S SER O G 54.029 52.378 22.957 1.00 53.87 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 2 . . . . . . P PRO N 52.447 55.004 22.388 1.00 33.37 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 2 . . . . . . P PRO C A 51.763 55.264 21.128 1.00 33.39 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 2 . . . . . . P PRO C 52.425 54.401 20.066 1.00 27.66 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 2 . . . . . . P PRO O 52.291 54.590 18.851 1.00 28.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 2 . . . . . . P PRO C B 52.034 56.746 20.799 1.00 35.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 2 . . . . . . P PRO C G 53.162 57.218 21.727 1.00 34.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 2 2 . . . . . . P PRO C D 53.218 56.209 22.865 1.00 33.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 3 . . . . . . G GLY N 53.208 53.487 20.565 1.00 20.99 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 3 . . . . . . G GLY C A 53.980 52.705 19.675 1.00 22.46 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 3 . . . . . . G GLY C 54.958 53.659 19.030 1.00 16.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 3 3 . . . . . . G GLY O 55.205 54.766 19.512 1.00 20.19 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 4 . . . . . . V VAL N 55.506 53.240 17.948 1.00 10.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 4 . . . . . . V VAL C A 56.416 54.088 17.282 1.00 15.89 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 4 . . . . . . V VAL C 55.625 55.088 16.453 1.00 17.74 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 4 . . . . . . V VAL O 54.828 54.675 15.629 1.00 15.36 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 4 . . . . . . V VAL C B 57.332 53.194 16.451 1.00 18.65 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 4 . . . . . . V VAL C G1 58.444 53.988 15.754 1.00 18.67 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 4 4 . . . . . . V VAL C G2 57.922 52.084 17.346 1.00 13.73 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 5 . . . . . . V VAL N 55.799 56.415 16.693 1.00 25.51 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 5 . . . . . . V VAL C A 55.049 57.431 15.929 1.00 20.42 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 5 . . . . . . V VAL C 55.655 57.849 14.605 1.00 21.66 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 5 . . . . . . V VAL O 56.846 58.112 14.504 1.00 31.38 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 5 . . . . . . V VAL C B 54.697 58.659 16.709 1.00 16.90 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 5 . . . . . . V VAL C G1 54.131 59.664 15.699 1.00 19.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 5 5 . . . . . . V VAL C G2 53.640 58.304 17.738 1.00 14.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 6 6 . . . . . . I ILE N 54.810 57.974 13.593 1.00 20.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 [Part of this file has been deleted for brevity] CO 1 1 . P 209 209 . . . . . . K LYS N 46.988 51.534 -7.357 1.00 39.61 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS C A 45.791 51.590 -6.554 1.00 41.75 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS C 44.610 51.650 -7.444 1.00 44.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS O 43.570 51.024 -7.222 1.00 47.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS C B 45.764 52.773 -5.656 1.00 41.31 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS C G 44.785 52.588 -4.531 1.00 40.21 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS C D 43.819 53.733 -4.515 1.00 44.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS C E 44.335 54.889 -5.365 1.00 49.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 209 209 . . . . . . K LYS N Z 44.965 55.969 -4.577 1.00 50.32 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 210 210 . . . . . . A ALA N 44.813 52.416 -8.475 1.00 43.71 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 210 210 . . . . . . A ALA C A 43.787 52.546 -9.446 1.00 41.88 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 210 210 . . . . . . A ALA C 43.831 51.390 -10.416 1.00 39.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 210 210 . . . . . . A ALA O 42.865 51.153 -11.085 1.00 48.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 210 210 . . . . . . A ALA C B 43.842 53.898 -10.151 1.00 40.52 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS N 44.935 50.644 -10.479 1.00 36.47 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS C A 45.123 49.543 -11.471 1.00 40.27 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS C 44.659 48.140 -11.033 1.00 41.97 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS O 44.458 47.243 -11.847 1.00 40.79 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS C B 46.560 49.545 -12.092 1.00 37.63 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS C G 47.140 48.161 -12.390 1.00 33.69 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS C D 48.551 47.914 -11.838 1.00 29.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS C E 49.678 48.306 -12.772 1.00 25.87 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 211 211 . . . . . . K LYS N Z 50.909 47.533 -12.545 1.00 26.93 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR N 44.581 47.951 -9.718 1.00 44.88 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C A 44.160 46.704 -9.076 1.00 42.88 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C 42.720 46.902 -8.639 1.00 46.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR O 42.495 47.283 -7.493 1.00 49.33 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C B 45.026 46.454 -7.772 1.00 35.96 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C G 46.478 46.111 -8.046 1.00 26.75 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C D1 46.745 45.100 -8.965 1.00 27.47 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C D2 47.556 46.816 -7.509 1.00 18.91 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C E1 48.037 44.766 -9.366 1.00 24.84 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C E2 48.858 46.511 -7.909 1.00 22.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR C Z 49.103 45.446 -8.787 1.00 25.50 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 212 212 . . . . . . Y TYR O H 50.377 45.086 -9.149 1.00 23.28 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS N 41.703 46.726 -9.463 1.00 48.75 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS C A 40.474 47.096 -8.795 1.00 60.15 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS C 39.248 46.226 -8.710 1.00 61.60 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS O 39.218 45.071 -9.141 1.00 68.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS C B 40.203 48.573 -8.682 1.00 73.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS C G 39.555 49.149 -9.926 1.00 82.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS C D 40.446 49.096 -11.156 1.00 88.26 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS C E 39.662 49.334 -12.441 1.00 93.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 213 213 . . . . . . K LYS N Z 40.403 50.145 -13.447 1.00 95.26 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 214 214 . . . . . . A ALA N 38.248 46.846 -8.067 1.00 57.39 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 214 214 . . . . . . A ALA C A 36.910 46.306 -7.804 1.00 53.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 214 214 . . . . . . A ALA C 35.963 46.427 -8.990 1.00 54.67 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 214 214 . . . . . . A ALA O 36.467 46.591 -10.145 1.00 53.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 214 214 . . . . . . A ALA C B 36.263 46.991 -6.605 1.00 49.58 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 214 214 . . . . . . A ALA O XT 34.731 46.398 -8.724 1.00 56.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 // Output file format The output is a standard EMBOSS report file. The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq. See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats. By default psiphi writes a 'table' format report file. Output files for usage example File: 1hmp_a.psiphi ######################################## # Program: psiphi # Rundate: Fri 15 Jul 2011 12:00:00 # Commandline: psiphi # [-infile] ../../data/1hmp_a.ccf # -chainnumber 1 # -startresiduenumber 5 # -finishresiduenumber 85 # Report_format: table # Report_file: 1hmp_a.psiphi ######################################## #======================================= # # Sequence: 1hmp_a from: 1 to: 214 # HitCount: 81 # # Chain: 1 # #======================================= Start End Score phi psi 5 5 0.0 -85.52 137.17 6 6 0.0 -124.99 85.24 7 7 0.0 -43.12 147.11 8 8 0.0 -48.31 -29.94 9 9 0.0 -88.16 -2.35 10 10 0.0 -52.85 130.05 11 11 0.0 -93.40 -4.97 12 12 0.0 79.02 -136.70 13 13 0.0 -149.38 150.69 14 14 0.0 -84.79 150.76 15 15 0.0 -46.26 -29.65 16 16 0.0 -58.90 -26.97 17 17 0.0 -93.04 -13.65 18 18 0.0 -121.01 177.67 19 19 0.0 -90.34 123.35 20 20 0.0 -137.24 150.01 21 21 0.0 -60.85 141.25 22 22 0.0 -68.94 -27.08 23 23 0.0 -71.26 -5.87 24 24 0.0 -124.07 13.09 25 25 0.0 -79.54 22.76 26 26 0.0 -145.15 -13.78 27 27 0.0 -95.38 4.02 28 28 0.0 -129.20 149.61 29 29 0.0 -90.42 -47.84 30 30 0.0 -162.69 160.59 31 31 0.0 -75.67 128.31 32 32 0.0 -96.18 -51.71 [Part of this file has been deleted for brevity] 38 38 0.0 -48.48 -63.46 39 39 0.0 -38.67 -55.32 40 40 0.0 -62.06 -37.43 41 41 0.0 -66.93 -47.14 42 42 0.0 -55.67 -36.42 43 43 0.0 -63.04 -44.39 44 44 0.0 -53.57 -57.37 45 45 0.0 -44.65 -49.45 46 46 0.0 -51.29 -42.54 47 47 0.0 -66.60 -39.52 48 48 0.0 -63.88 -48.01 49 49 0.0 -56.50 -52.92 50 50 0.0 -62.39 -18.62 51 51 0.0 -56.19 -46.58 52 52 0.0 -86.42 -51.81 53 53 0.0 -88.19 -25.17 54 54 0.0 -56.43 151.52 55 55 0.0 85.66 9.25 56 56 0.0 -139.15 162.01 57 57 0.0 -65.45 110.45 58 58 0.0 -101.25 138.36 59 59 0.0 -105.46 112.70 60 60 0.0 -93.70 115.62 61 61 0.0 -108.38 131.59 62 62 0.0 -109.96 130.63 63 63 0.0 -94.00 109.57 64 64 0.0 -93.72 67.41 65 65 0.0 -65.62 -102.57 66 66 0.0 -109.14 11.70 67 67 0.0 -170.15 178.49 68 68 0.0 -125.12 -30.99 69 69 0.0 -36.99 -53.96 70 70 0.0 -62.26 -46.94 71 71 0.0 -50.46 -58.23 72 72 0.0 -51.09 -52.57 73 73 0.0 -56.83 -50.75 74 74 0.0 -55.14 -51.03 75 75 0.0 -54.01 -32.78 76 76 0.0 -64.26 -33.38 77 77 0.0 -73.24 -38.25 78 78 0.0 -67.12 -50.61 79 79 0.0 -47.17 -56.48 80 80 0.0 -49.34 -24.22 81 81 0.0 -90.53 -27.37 82 82 0.0 -79.04 3.07 83 83 0.0 -72.14 -34.64 84 84 0.0 -78.17 -5.83 85 85 0.0 -70.69 142.19 #--------------------------------------- #--------------------------------------- Data files Notes Clean coordinate file (CCF) of protein structure coordinates are generated by running pdbparse (in the 'structure' EMBASSY package) on a PDB file. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description Author(s) Damian Counsell formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None