Hi, Hope this is the correct place for this question :)
I have a pdb file with many small fragments in addition to a longer chain. These are not numerated in any way, only separated by TER (example below). In pymol, only two 'chains' appear, one with the long chain, and the other with all the fragments mixed together. Do chains need to be separated by anything else than lines containing TER? If I try to visualise the same pdb file in rasmol, the separate chains are drawn up (for instance with ribbon). Also, is there a limit to how many chains pymol can handle? I might have 1000 shorter chains in one pdb file. I run pymol 0.99rc6 for linux. Any help appreciated :) Sincerly, Siv Hollup Example file: ATOM 1 CA ALA A 2 39.866 21.059 8.959 1.00 0.000 ATOM 2 CA ASP A 3 43.425 19.735 8.836 1.00 0.000 ATOM 3 CA LYS A 4 44.119 17.105 6.147 1.00 0.000 ATOM 4 CA GLU A 5 45.918 15.101 8.820 1.00 0.000 ATOM 5 CA LEU A 6 42.800 14.764 10.998 1.00 0.000 ATOM 6 CA LYS A 7 42.788 11.087 12.105 1.00 0.000 ATOM 7 CA PHE A 8 39.620 9.225 11.057 1.00 0.000 ATOM 8 CA LEU A 9 38.249 5.964 12.522 1.00 0.000 ATOM 9 CA VAL A 10 36.051 4.078 9.925 1.00 0.000 ATOM 10 CA VAL A 11 33.741 1.537 11.645 1.00 0.000 ATOM 11 CA ASP A 12 31.811 -1.156 9.804 1.00 0.000 ATOM 12 CA ASP A 13 31.552 -4.975 9.930 1.00 0.000 ATOM 13 CA PHE A 14 32.160 -5.228 6.162 1.00 0.000 ATOM 14 CA SER A 15 35.826 -4.868 5.227 1.00 0.000 ATOM 15 CA THR A 16 34.876 -3.922 1.618 1.00 0.000 ATOM 16 CA MET A 17 32.758 -0.963 2.790 1.00 0.000 ATOM 17 CA ARG A 18 35.630 0.118 5.108 1.00 0.000 ATOM 18 CA ARG A 19 37.960 0.012 2.052 1.00 0.000 ATOM 19 CA ILE A 20 35.480 2.111 0.006 1.00 0.000 ATOM 20 CA VAL A 21 35.304 4.818 2.693 1.00 0.000 ATOM 21 CA ARG A 22 39.075 4.807 3.161 1.00 0.000 <znip long chain> ATOM 121 CA LYS A 122 28.602 20.659 6.335 1.00 0.000 ATOM 122 CA ILE A 123 29.836 19.118 9.608 1.00 0.000 ATOM 123 CA PHE A 124 33.045 21.152 9.650 1.00 0.000 ATOM 124 CA GLU A 125 30.917 24.274 9.124 1.00 0.000 ATOM 125 CA LYS A 126 28.302 23.283 11.765 1.00 0.000 ATOM 126 CA LEU A 127 31.094 22.603 14.304 1.00 0.000 ATOM 127 CA GLY A 128 33.194 25.622 13.408 1.00 0.000 ATOM 128 CA MET A 129 36.197 23.497 12.226 1.00 0.000 TER REMARK next fragment ATOM 1 CA ASP 928 42.867 13.075 13.193 1.00 1.00 ATOM 2 CA VAL 929 41.607 9.565 12.506 1.00 2.00 ATOM 3 CA ILE 930 38.318 8.385 11.059 1.00 4.00 ATOM 4 CA LEU 931 37.131 4.823 11.752 1.00 8.00 ATOM 5 CA LEU 932 34.886 4.133 8.729 1.00 4.00 ATOM 6 CA LEU 933 32.669 1.190 9.618 1.00 2.00 ATOM 7 CA ASP 934 30.966 -1.045 7.090 1.00 1.00 ATOM 8 CA LYS 948 31.343 -1.115 17.238 1.00 1.00 ATOM 9 CA SER 949 33.588 -3.020 19.694 1.00 2.00 ATOM 10 CA PHE 950 36.575 -2.337 17.454 1.00 3.00 ATOM 11 CA ALA 951 35.721 1.386 17.478 1.00 4.00 ATOM 12 CA LYS 952 35.265 1.425 21.266 1.00 3.00 ATOM 13 CA ALA 953 38.537 -0.417 21.936 1.00 2.00 ATOM 14 CA PHE 954 40.407 1.905 19.558 1.00 1.00 ATOM 15 CA ALA 951 35.721 1.386 17.478 1.00 1.00 ATOM 16 CA LYS 952 35.265 1.425 21.266 1.00 2.00 ATOM 17 CA ALA 953 38.537 -0.417 21.936 1.00 3.00 ATOM 18 CA PHE 954 40.407 1.905 19.558 1.00 4.00 ATOM 19 CA ILE 955 38.981 4.961 21.371 1.00 3.00 ATOM 20 CA SER 956 39.800 3.586 24.844 1.00 2.00 ATOM 21 CA LYS 957 43.410 2.919 23.826 1.00 1.00 ATOM 22 CA LYS 952 35.265 1.425 21.266 1.00 1.00 ATOM 23 CA ALA 953 38.537 -0.417 21.936 1.00 2.00 ATOM 24 CA PHE 954 40.407 1.905 19.558 1.00 3.00 ATOM 25 CA ILE 955 38.981 4.961 21.371 1.00 4.00 ATOM 26 CA SER 956 39.800 3.586 24.844 1.00 3.00 ATOM 27 CA LYS 957 43.410 2.919 23.826 1.00 2.00 ATOM 28 CA ALA 958 43.936 6.085 21.764 1.00 1.00 TER <znip many more fragments> -- Siv Midtun Hollup PhD Student Dept. of Informatics University of Bergen, Norway s...@ii.uib.no (NOTE: new email adress) - Blessed are the flexible, for they can be tied into knots. -
