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HELP in questions and answers on the AbIni program
Q: For what purpose the program is intended? Example: ======================================================================================== ***** SET 1 ***** >1NDDB qb=0 pb=25 le=20 Sc=98.9 aaaa bbbbb MSANFTDKNGRQSKGVLLLR IKERVEEKEGIPPQQQRLIY aaaaaaaaa bbbbb ATOM 794 N ILE B 126 37.162 -0.022 40.293 1.00 12.67 N ATOM 795 CA ILE B 126 35.962 -0.674 39.781 1.00 11.72 C ATOM 796 C ILE B 126 35.671 -0.073 38.399 1.00 12.39 C ATOM 797 O ILE B 126 35.366 -0.799 37.452 1.00 14.47 O ATOM 798 CB ILE B 126 34.746 -0.424 40.696 1.00 13.18 C ATOM 799 CG1 ILE B 126 35.033 -0.951 42.107 1.00 14.02 C ATOM 800 CG2 ILE B 126 33.499 -1.074 40.094 1.00 15.53 C ATOM 801 CD1 ILE B 126 33.908 -0.706 43.107 1.00 14.94 C ATOM 802 N LYS B 127 35.806 1.249 38.282 1.00 11.60 N ATOM 803 CA LYS B 127 35.581 1.929 37.006 1.00 11.37 C .... ... .. ... . ... ...... ..... ...... .... ..... . ATOM 964 CZ TYR B 145 25.681 -2.498 47.587 1.00 17.99 C ATOM 965 OH TYR B 145 25.481 -3.704 48.220 1.00 20.22 O >2PDZA qb=20 pb=31 le=17 Sc=93.1 b TLAMPSDTNANGDIFGG KIFKGLAADQTEALFVG b aaaa ATOM 498 N LYS A 32 -1.097 -3.476 -1.916 1.00 0.00 N .... ... .. ... . ... ...... ..... ...... .... ..... . TER ======================================================================================== There may be several variants of coverings (SETs); therefore, each new variant starts from the corresponding keyword, for example, "SET 1"; next, "SET 2"; etc.
Q: How is it possible to create a COV file?
Example: suppose, you want to "disrupt" the native structure of a protein (and you have this structure in PDB format) to test then how it will be restored using this program. For this purpose, copy your PDB file, for example, YourProtein.pdb, into the file with a name, for example, YourProtein.cov, and introduce the corresponding changes:
Example: ******* SET 1 ******* REMARK MSI WebLab Viewer PDB file REMARK Created: Fri Oct 25 07:58:42 ÇÈܪ¨ÒÙ¹ÜÒ LÞÛ (ÞÛØÒ) 2002 CRYST1 57.810 29.700 106.090 90.00 101.99 90.00 A2 ATOM 1 N GLY A 1 15.740 11.178 -11.733 1.00 0.00 ATOM 2 CA GLY A 1 15.234 10.462 -10.556 1.00 0.00 ATOM 3 C GLY A 1 16.284 9.483 -9.998 1.00 0.00 ATOM 4 O GLY A 1 17.150 8.979 -10.709 1.00 0.00 .... ... .. ... . ... ...... ..... ...... .... ..... ATOM 310 N LEU A 40 6.658 -4.909 19.830 1.00 0.00 ATOM 311 CA LEU A 40 6.751 -5.839 20.961 1.00 0.00 ATOM 312 C LEU A 40 5.510 -6.747 21.050 1.00 0.00 ATOM 313 O LEU A 40 5.642 -7.969 21.132 1.00 0.00 ATOM 314 CB LEU A 40 6.968 -5.086 22.286 1.00 0.00 ATOM 315 CG LEU A 40 7.926 -5.898 23.179 1.00 0.00 ATOM 316 CD1 LEU A 40 8.886 -4.973 23.944 1.00 0.00 ATOM 317 CD2 LEU A 40 7.121 -6.784 24.145 1.00 0.00 // Empty line - a point of a break ATOM 318 N GLU A 41 4.357 -6.093 21.040 1.00 0.00 ATOM 319 CA GLU A 41 3.066 -6.778 21.082 1.00 0.00 ATOM 320 C GLU A 41 2.967 -7.863 19.997 1.00 0.00 ATOM 321 O GLU A 41 2.821 -9.046 20.315 1.00 0.00 ATOM 322 CB GLU A 41 1.903 -5.775 20.992 1.00 0.00 ATOM 323 CG GLU A 41 1.986 -4.741 22.132 1.00 0.00 ATOM 324 CD GLU A 41 0.577 -4.464 22.689 1.00 0.00 ATOM 325 OE1 GLU A 41 -0.227 -5.435 22.661 1.00 0.00 ATOM 326 OE2 GLU A 41 0.371 -3.298 23.120 1.00 0.00 TER |
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