Hi Marek, Not to my knowledge. In my tests, this is written out from Chimera with HETATM lines instead of ATOM, which already means that the residues should not be connected to each other automatically. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 21, 2017, at 4:03 PM, Marek Maly <marek.maly@ujep.cz> wrote:
Hello,
is it possible to save the given molecular model (which is open in Chimera) in PDB format but with the TER string between consequent residues ?
example: --------------------------- ATOM 1 Si1 CEN A 1 56.395 15.633 50.147 1.00 0.00 Si TER ATOM 2 C1 RE1 A 2 54.892 16.772 50.453 1.00 0.00 C ATOM 3 H1 RE1 A 2 54.289 16.821 49.538 1.00 0.00 H ATOM 4 H2 RE1 A 2 54.219 16.552 51.290 1.00 0.00 H ATOM 5 C2 RE1 A 2 55.394 18.185 50.780 1.00 0.00 C ATOM 6 H3 RE1 A 2 55.896 18.665 49.932 1.00 0.00 H ATOM 7 H4 RE1 A 2 56.038 18.053 51.659 1.00 0.00 H ATOM 8 C3 RE1 A 2 54.181 19.075 51.202 1.00 0.00 C ATOM 9 H6 RE1 A 2 53.674 18.496 51.984 1.00 0.00 H ATOM 10 H5 RE1 A 2 53.589 19.325 50.313 1.00 0.00 H ATOM 11 Si3 RE1 A 2 54.714 20.646 51.949 1.00 0.00 Si ATOM 12 C4 RE1 A 2 53.140 21.420 52.746 1.00 0.00 C ATOM 13 H8 RE1 A 2 53.430 22.271 53.376 1.00 0.00 H ATOM 14 H7 RE1 A 2 52.690 20.675 53.413 1.00 0.00 H ATOM 15 H9 RE1 A 2 52.466 21.649 51.911 1.00 0.00 H ATOM 16 C5 RE1 A 2 55.491 21.841 50.620 1.00 0.00 C ATOM 17 H12 RE1 A 2 56.423 21.426 50.217 1.00 0.00 H ATOM 18 H10 RE1 A 2 55.768 22.733 51.196 1.00 0.00 H ATOM 19 H11 RE1 A 2 54.875 22.300 49.836 1.00 0.00 H TER ATOM 20 C1 RE1 A 3 57.436 16.272 48.673 1.00 0.00 C ATOM 21 H1 RE1 A 3 58.039 17.117 49.028 1.00 0.00 H ATOM 22 H2 RE1 A 3 58.209 15.633 48.228 1.00 0.00 H ATOM 23 C2 RE1 A 3 56.488 16.820 47.464 1.00 0.00 C ATOM 24 H3 RE1 A 3 55.675 17.467 47.819 1.00 0.00 H ATOM 25 H4 RE1 A 3 55.960 16.034 46.910 1.00 0.00 H ATOM 26 C3 RE1 A 3 57.354 17.603 46.475 1.00 0.00 C ATOM 27 H6 RE1 A 3 58.241 17.015 46.210 1.00 0.00 H ATOM 28 H5 RE1 A 3 57.812 18.464 46.978 1.00 0.00 H ATOM 29 Si3 RE1 A 3 56.645 18.300 44.851 1.00 0.00 Si ATOM 30 C4 RE1 A 3 55.474 17.030 44.146 1.00 0.00 C ATOM 31 H8 RE1 A 3 54.666 17.578 43.646 1.00 0.00 H ATOM 32 H7 RE1 A 3 54.864 16.542 44.918 1.00 0.00 H ATOM 33 H9 RE1 A 3 55.893 16.349 43.396 1.00 0.00 H ATOM 34 C5 RE1 A 3 58.034 18.987 43.812 1.00 0.00 C ATOM 35 H12 RE1 A 3 59.000 18.584 44.141 1.00 0.00 H ATOM 36 H10 RE1 A 3 58.180 20.062 43.974 1.00 0.00 H ATOM 37 H11 RE1 A 3 58.009 18.601 42.786 1.00 0.00 H TER ATOM 38 C1 RE1 A 4 57.426 15.522 51.783 1.00 0.00 C ATOM 39 H1 RE1 A 4 58.370 14.991 51.606 1.00 0.00 H ATOM 40 H2 RE1 A 4 57.769 16.539 52.007 1.00 0.00 H ATOM 41 C2 RE1 A 4 56.787 14.966 52.995 1.00 0.00 C ATOM 42 H3 RE1 A 4 57.587 14.881 53.741 1.00 0.00 H ATOM 43 H4 RE1 A 4 56.321 13.982 52.869 1.00 0.00 H ATOM 44 C3 RE1 A 4 55.776 15.938 53.682 1.00 0.00 C ATOM 45 H6 RE1 A 4 54.722 15.759 53.439 1.00 0.00 H ATOM 46 H5 RE1 A 4 55.920 17.004 53.467 1.00 0.00 H ATOM 47 Si3 RE1 A 4 55.756 16.172 55.603 1.00 0.00 Si ATOM 48 C4 RE1 A 4 57.359 16.942 56.191 1.00 0.00 C ATOM 49 H8 RE1 A 4 57.601 17.853 55.629 1.00 0.00 H ATOM 50 H7 RE1 A 4 58.242 16.306 56.061 1.00 0.00 H ATOM 51 H9 RE1 A 4 57.248 17.148 57.263 1.00 0.00 H ATOM 52 C5 RE1 A 4 55.827 14.369 56.251 1.00 0.00 C ATOM 53 H12 RE1 A 4 56.581 13.702 55.818 1.00 0.00 H ATOM 54 H10 RE1 A 4 54.854 13.866 56.186 1.00 0.00 H ATOM 55 H11 RE1 A 4 56.205 14.393 57.280 1.00 0.00 H TER . . . ---------------------------
If yes, how to do it ?
Thank you in advance for your advice.
Best wishes,
Marek