![]() |
psiphi |
% psiphi 1atn.pxyz -chainnumber=2 -startresiduenumber=4 -finishresiduenumber=65 -outf=1atn.psiphi Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-infile] infile Clean coordinate file -chainnumber integer Number of the chain for which torsion angles should be calculated -startresiduenumber integer First residue in chain for which torsion angles should be calculated -finishresiduenumber integer Last residue in chain for which torsion angles should be calculated (1 = last residue) [-outfile] report 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 -rusashow2 boolean Show the full USA in the report General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-infile] (Parameter 1) |
Clean coordinate 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 | |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
ID 1atn XX DE DEOXYRIBONUCLEASE I COMPLEX WITH ACTIN XX OS ACTIN FROM RABBIT (ORYCTOLAGUS $CUNICULUS) MUSCLE, DEOXYRIBONUCLEASE I FROM OS BOVINE (BOS $TAURUS) PANCREAS XX EX METHOD xray; RESO 2.80; NMOD 1; NCHA 2; NGRP 0; XX CN [1] XX IN ID A; NR 373; NL 1; NH 0; NE 0; XX SQ SEQUENCE 373 AA; 41549 MW; DC8866DE CRC32; XDEDETTALV CDNGSGLVKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIEHGIITNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV THNVPIYEGY ALPHAIMRLD LAGRDLTDYL MKILTERGYS FVTTAEREIV RDIKEKLCYV ALDFENEMAT AASSSSLEKS YELPDGQVIT IGNERFRCPE TLFQPSFIGM ESAGIHETTY NSIMKCDIDI RKDLYANNVM SGGTTMYPGI ADRMQKEITA LAPSTMKIKI IAPPERKYSV WIGGSILASL STFQQMWITK QEYDEAGPSI VHR XX CN [2] XX IN ID D; NR 260; NL 4; NH 0; NE 0; XX SQ SEQUENCE 260 AA; 29021 MW; CF3AF818 CRC32; LKIAAFNIRT FGETKMSNAT LASYIVRIVR RYDIVLIQEV RDSHLVAVGK LLDYLNQDDP NTYHYVVSEP LGRNSYKERY LFLFRPNKVS VLDTYQYDDG CGNCGNDSFS REPAVVKFSS HSTKVKEFAI VALHSAPSDA VAEINSLYDV YLDVQQKWHL NDVMLMGDFN ADCSYVTSSQ WSSIRLRTSS TFQWLIPDSA DTTATSTNCA YDRIVVAGSL LQSSVVPGSA APFDFQAAYG LSNEMALAIS DHYPVEVTLT XX CO 1 1 . P 1 0 . . . . . . X ACE CA 105.046 51.546 40.626 1.00 72.72 0.00 0.00 0.00 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 0 . . . . . . X ACE C 105.314 50.822 41.951 1.00 72.72 0.00 0.00 0.00 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 0 . . . . . . X ACE O 105.220 51.451 43.013 1.00 72.56 0.00 0.00 0.00 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 1 . . . . . . D ASP N 105.665 49.507 41.867 1.00 71.64 0.00 0.00 0.00 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 1 . . . . . . D ASP CA 105.992 48.589 42.982 1.00 70.20 0.00 0.00 0.00 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 1 . . . . . . D ASP C 107.024 49.191 43.936 1.00 69.70 0.00 0.00 0.00 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 1 . . . . . . D ASP O 106.927 49.088 45.163 1.00 69.14 0.00 0.00 0.00 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 1 . . . . . . D ASP CB 106.533 47.248 42.410 1.00 70.66 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 1 . . . . . . D ASP CG 106.801 46.077 43.383 1.00 71.73 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 2 1 . . . . . . D ASP OD1 107.722 46.143 44.215 1.00 71.57 0.00 0.00 0.00 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 1 . . . . . . D ASP OD2 106.092 45.066 43.291 1.00 71.25 0.00 0.00 0.00 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 2 . . . . . . E GLU N 107.976 49.873 43.293 1.00 69.24 0.00 0.00 0.00 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 2 . . . . . . E GLU CA 109.054 50.658 43.886 1.00 69.94 0.00 0.00 0.00 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 2 . . . . . . E GLU C 108.707 51.166 45.277 1.00 69.71 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 3 2 . . . . . . E GLU O 109.454 51.029 46.250 1.00 69.74 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 3 2 . . . . . . E GLU CB 109.372 51.861 42.969 1.00 69.58 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 3 2 . . . . . . E GLU CG 110.164 51.624 41.669 1.00 68.60 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 [Part of this file has been deleted for brevity] CO 1 2 1 H . 19 . . . . . . . NAG O4 98.227 34.053 113.446 1.00 64.85 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 1 H . 19 . . . . . . . NAG O5 100.413 31.985 111.201 1.00 54.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 1 H . 19 . . . . . . . NAG O6 97.994 32.836 109.744 1.00 59.46 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 2 1 H . 19 . . . . . . . NAG O7 103.385 35.944 112.239 1.00 55.99 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 2 2 H . 20 . . . . . . . MAN C1 96.772 33.881 113.379 1.00 68.38 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 2 2 H . 20 . . . . . . . MAN C2 96.423 32.389 113.835 1.00 70.26 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 2 2 H . 20 . . . . . . . MAN C3 94.879 32.118 113.838 1.00 70.54 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 2 2 H . 20 . . . . . . . MAN C4 94.053 33.398 114.389 1.00 69.85 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 2 H . 20 . . . . . . . MAN C5 94.592 34.841 113.979 1.00 68.53 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 2 H . 20 . . . . . . . MAN C6 94.002 35.946 114.874 1.00 68.79 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 2 2 H . 20 . . . . . . . MAN O2 96.914 32.017 115.162 1.00 72.48 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 2 2 H . 20 . . . . . . . MAN O3 94.659 30.955 114.705 1.00 70.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 2 H . 20 . . . . . . . MAN O4 92.653 33.295 113.978 1.00 67.74 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 2 2 H . 20 . . . . . . . MAN O5 96.045 34.932 114.115 1.00 68.39 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 2 2 H . 20 . . . . . . . MAN O6 93.433 35.451 116.094 1.00 66.54 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 2 3 H . 1 . . . . . . . ATP PG 94.786 57.032 71.655 1.00 17.67 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 2 3 H . 1 . . . . . . . ATP O1G 93.888 57.203 72.813 1.00 17.23 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP O2G 94.087 56.937 70.331 1.00 18.23 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP O3G 95.936 57.949 71.667 1.00 13.03 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 2 3 H . 1 . . . . . . . ATP PB 95.420 54.238 70.875 1.00 17.65 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 2 3 H . 1 . . . . . . . ATP O1B 95.408 54.672 69.455 1.00 17.84 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 2 3 H . 1 . . . . . . . ATP O2B 96.550 53.385 71.257 1.00 16.43 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP O3B 95.434 55.566 71.804 1.00 17.15 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 2 3 H . 1 . . . . . . . ATP PA 93.252 52.426 70.371 1.00 14.57 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP O1A 92.117 53.068 69.684 1.00 17.79 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 2 3 H . 1 . . . . . . . ATP O2A 94.234 51.707 69.559 1.00 15.67 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 2 3 H . 1 . . . . . . . ATP O3A 94.040 53.512 71.217 1.00 14.88 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 2 3 H . 1 . . . . . . . ATP O5* 92.578 51.370 71.396 1.00 16.54 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 2 3 H . 1 . . . . . . . ATP C5* 93.252 50.711 72.492 1.00 18.27 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 2 3 H . 1 . . . . . . . ATP C4* 92.460 50.926 73.755 1.00 19.17 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP O4* 91.144 50.564 73.360 1.00 20.56 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP C3* 92.722 50.104 75.040 1.00 20.09 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 2 3 H . 1 . . . . . . . ATP O3* 92.087 50.587 76.224 1.00 17.92 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 2 3 H . 1 . . . . . . . ATP C2* 91.959 48.850 74.668 1.00 20.89 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 2 3 H . 1 . . . . . . . ATP O2* 91.527 48.031 75.744 1.00 21.55 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP C1* 90.679 49.466 74.154 1.00 21.41 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP N9 89.918 48.445 73.348 1.00 21.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP C8 90.398 47.620 72.338 1.00 21.06 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 2 3 H . 1 . . . . . . . ATP N7 89.510 46.748 71.915 1.00 20.71 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 2 3 H . 1 . . . . . . . ATP C5 88.413 46.916 72.781 1.00 16.60 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 2 3 H . 1 . . . . . . . ATP C6 87.170 46.213 72.863 1.00 14.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP N6 86.856 45.101 72.189 1.00 9.78 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP N1 86.253 46.764 73.722 1.00 13.84 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 2 3 H . 1 . . . . . . . ATP C2 86.612 47.919 74.399 1.00 15.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP N3 87.800 48.496 74.561 1.00 15.64 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 3 H . 1 . . . . . . . ATP C4 88.626 48.004 73.609 1.00 17.21 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 2 4 H . 2 . . . . . . . CA CA 94.454 56.550 67.891 1.00 32.57 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 4 H . 3 . . . . . . . CA CA 114.215 17.675 107.885 1.00 7.01 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 2 4 H . 4 . . . . . . . CA CA 112.657 20.573 78.226 1.00 19.23 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 2 4 H . 5 . . . . . . . CA CA 119.545 10.433 103.688 1.00 46.63 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 // |
######################################## # Program: psiphi # Rundate: Thu Jul 15 2004 12:00:00 # Report_format: table # Report_file: 1atn.psiphi ######################################## #======================================= # # Sequence: from: 1 to: 260 # HitCount: 62 # # Chain: 2 # #======================================= Start End Score phi psi 4 4 0.0 -152.91 162.88 5 5 0.0 -129.90 132.52 6 6 0.0 -142.63 113.29 7 7 0.0 -91.20 109.22 8 8 0.0 -99.20 117.89 9 9 0.0 -56.16 115.60 10 10 0.0 57.98 45.32 11 11 0.0 -59.93 122.46 12 12 0.0 -160.93 -176.93 13 13 0.0 -55.71 -39.72 14 14 0.0 -67.65 -49.61 15 15 0.0 -63.01 -41.04 16 16 0.0 -71.25 -23.04 17 17 0.0 -69.32 -27.48 18 18 0.0 -71.35 139.52 19 19 0.0 -80.91 -39.47 20 20 0.0 -66.20 -52.09 21 21 0.0 -58.24 -49.39 22 22 0.0 -55.11 -37.72 23 23 0.0 -69.44 -26.56 24 24 0.0 -89.18 -40.94 25 25 0.0 -58.18 -50.57 26 26 0.0 -55.42 -35.34 27 27 0.0 -75.89 -29.61 28 28 0.0 -73.06 -47.91 29 29 0.0 -58.27 -39.38 30 30 0.0 -74.40 7.40 31 31 0.0 -88.83 -12.94 32 32 0.0 -112.19 143.00 33 33 0.0 -83.95 -22.06 34 34 0.0 -139.78 125.86 35 35 0.0 -130.67 137.57 36 36 0.0 -111.45 130.80 37 37 0.0 -122.64 128.08 38 38 0.0 -107.31 161.06 39 39 0.0 69.88 33.76 40 40 0.0 -78.38 95.67 41 41 0.0 -100.44 80.73 42 42 0.0 -131.78 103.94 43 43 0.0 -71.07 -45.38 44 44 0.0 -98.79 -4.45 45 45 0.0 75.81 20.16 46 46 0.0 -65.57 -34.72 47 47 0.0 -76.51 -33.90 48 48 0.0 -69.12 -40.81 49 49 0.0 -52.66 -49.63 50 50 0.0 -66.30 -36.64 51 51 0.0 -67.41 -40.85 52 52 0.0 -74.64 -31.01 53 53 0.0 -55.01 -50.20 54 54 0.0 -54.59 -54.81 55 55 0.0 -67.07 -26.37 56 56 0.0 -114.18 26.44 57 57 0.0 -71.15 -21.29 58 58 0.0 -116.13 -27.89 59 59 0.0 -120.69 134.74 60 60 0.0 -67.87 -18.39 61 61 0.0 -121.37 38.83 62 62 0.0 -64.44 -32.21 63 63 0.0 -145.31 135.69 64 64 0.0 -115.03 154.92 65 65 0.0 -120.22 167.29 #--------------------------------------- #--------------------------------------- |
Program name | Description |
---|