📄 psiphi.txt
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psiphi Function Phi and psi torsion angles from protein coordinatesDescription Calculates the psi and phi torsion angles around the alpha carbons (CA) in (a specified stretch of) a specified chain of a protein structure from the co-ordinates of the mainchain atoms in the two planes around itAlgorithmUsage Here is a sample session with psiphi% psiphi 1hmp_a.ccf -chainnumber=1 -startresiduenumber=5 -finishresiduenumber=85 Phi and psi torsion angles from protein coordinatesOutput report [1hmp_a.psiphi]: Go to the input files for this example Go to the output files for this exampleCommand 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 -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 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 dying program messagesInput file format psiphi reads ... Input files for usage example File: 1hmp_a.ccfID 1hmp_aXXDE .XXOS .XXEX METHOD xray; RESO 2.50; NMOD 1; NCHN 1; NGRP 0;XXCN [1]XXIN ID A; NR 214; NL 0; NH 0; NE 0;XXSQ 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 KYKAXXCO 1 1 . P 1 1 . . . . . . S SERN 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 0.00CO 1 1 . P 1 1 . . . . . . S SERCA 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 0.00CO 1 1 . P 1 1 . . . . . . S SERC 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 0.00CO 1 1 . P 1 1 . . . . . . S SERO 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 0.00CO 1 1 . P 1 1 . . . . . . S SERCB 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 0.00CO 1 1 . P 1 1 . . . . . . S SEROG 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 0.00CO 1 1 . P 2 2 . . . . . . P PRON 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 0.00CO 1 1 . P 2 2 . . . . . . P PROCA 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 0.00CO 1 1 . P 2 2 . . . . . . P PROC 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 0.00CO 1 1 . P 2 2 . . . . . . P PROO 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 0.00CO 1 1 . P 2 2 . . . . . . P PROCB 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 0.00CO 1 1 . P 2 2 . . . . . . P PROCG 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 0.00CO 1 1 . P 2 2 . . . . . . P PROCD 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 0.00CO 1 1 . P 3 3 . . . . . . G GLYN 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 0.00CO 1 1 . P 3 3 . . . . . . G GLYCA 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 0.00CO 1 1 . P 3 3 . . . . . . G GLYC 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 0.00CO 1 1 . P 3 3 . . . . . . G GLYO 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 0.00CO 1 1 . P 4 4 . . . . . . V VALN 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 0.00CO 1 1 . P 4 4 . . . . . . V VALCA 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 0.00CO 1 1 . P 4 4 . . . . . . V VALC 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 0.00CO 1 1 . P 4 4 . . . . . . V VALO 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 0.00CO 1 1 . P 4 4 . . . . . . V VALCB 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 0.00CO 1 1 . P 4 4 . . . . . . V VALCG1 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 0.00CO 1 1 . P 4 4 . . . . . . V VALCG2 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 0.00CO 1 1 . P 5 5 . . . . . . V VALN 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 0.00CO 1 1 . P 5 5 . . . . . . V VALCA 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 0.00CO 1 1 . P 5 5 . . . . . . V VALC 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 0.00CO 1 1 . P 5 5 . . . . . . V VALO 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 0.00CO 1 1 . P 5 5 . . . . . . V VALCB 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 0.00CO 1 1 . P 5 5 . . . . . . V VALCG1 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 0.00CO 1 1 . P 5 5 . . . . . . V VALCG2 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 0.00CO 1 1 . P 6 6 . . . . . . I ILEN 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 LYSN 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSCA 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSC 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSO 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSCB 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSCG 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSCD 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSCE 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 0.00CO 1 1 . P 209 209 . . . . . . K LYSNZ 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 0.00CO 1 1 . P 210 210 . . . . . . A ALAN 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 0.00CO 1 1 . P 210 210 . . . . . . A ALACA 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 0.00CO 1 1 . P 210 210 . . . . . . A ALAC 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 0.00CO 1 1 . P 210 210 . . . . . . A ALAO 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 0.00CO 1 1 . P 210 210 . . . . . . A ALACB 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 0.00CO 1 1 . P 211 211 . . . . . . K LYSN 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 0.00CO 1 1 . P 211 211 . . . . . . K LYSCA 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⌨️ 快捷键说明
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